From 82bea4d50fca5b702cb6fdca2734babe2f84e428 Mon Sep 17 00:00:00 2001 From: zxBIB Schcolnicov Date: Mon, 19 Aug 2024 16:57:22 +0200 Subject: [PATCH 01/15] Initialized tests --- .github/workflows/ci.yml | 99 ++++++++++--- .gitignore | 1 + nf-test.config | 16 +++ tests/lib/UTILS.groovy | 11 ++ tests/test.nf.test | 263 +++++++++++++++++++++++++++++++++++ tests/test_index.nf.test | 229 ++++++++++++++++++++++++++++++ tests/test_no_genome.nf.test | 262 ++++++++++++++++++++++++++++++++++ tests/test_umi.nf.test | 184 ++++++++++++++++++++++++ 8 files changed, 1047 insertions(+), 18 deletions(-) create mode 100644 nf-test.config create mode 100644 tests/lib/UTILS.groovy create mode 100644 tests/test.nf.test create mode 100644 tests/test_index.nf.test create mode 100644 tests/test_no_genome.nf.test create mode 100644 tests/test_umi.nf.test diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index dcbd4ff0..a9c1e13c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,37 +1,56 @@ name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: - push: - branches: - - dev pull_request: - release: - types: [published] env: NXF_ANSI_LOG: false + NFT_VER: "0.8.4" + NFT_WORKDIR: "~" + NFT_DIFF: "pdiff" + NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true - jobs: + nf-test-changes: + name: Check for changes + runs-on: ubuntu-latest + outputs: + nf_test_files: ${{ steps.list.outputs.components }} + steps: + - uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: List nf-test files + id: list + uses: adamrtalbot/detect-nf-test-changes@v0.0.2 + with: + head: ${{ github.sha }} + base: origin/${{ github.base_ref }} + include: .github/include.yaml + + - name: print list of nf-test files + run: | + echo ${{ steps.list.outputs.components }} + test: - name: Run pipeline with test data - # Only run on push if this is the nf-core dev branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/smrnaseq') }}" + name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }} + needs: [nf-test-changes] + if: needs.nf-test-changes.outputs.nf_test_files != '[]' runs-on: ubuntu-latest strategy: fail-fast: false matrix: NXF_VER: - - "23.04.0" - "latest-everything" + - "23.04" + nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] profile: - - "test" - - "test_no_genome" - - "test_umi" - - "test_index" + - "docker" + steps: - name: Check out pipeline code uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 @@ -41,9 +60,53 @@ jobs: with: version: "${{ matrix.NXF_VER }}" - - name: Disk space cleanup - uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 + - uses: actions/setup-python@v4 + with: + python-version: "3.11" + architecture: "x64" + + - name: Install pdiff to see diff between nf-test snapshots + run: | + python -m pip install --upgrade pip + pip install pdiff + + - uses: nf-core/setup-nf-test@v1 + + - name: Run nf-test + run: | + nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap + + - uses: pcolby/tap-summary@v1 + with: + path: >- + test.tap + + - name: Output log on failure + if: failure() + run: | + sudo apt install bat > /dev/null + batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log + + - name: Publish Test Report + uses: mikepenz/action-junit-report@v3 + if: always() # always run even if the previous step fails + with: + report_paths: test.xml + + confirm-pass: + runs-on: ubuntu-latest + needs: [test] + if: always() + steps: + - name: All tests ok + if: ${{ !contains(needs.*.result, 'failure') }} + run: exit 0 + - name: One or more tests failed + if: ${{ contains(needs.*.result, 'failure') }} + run: exit 1 - - name: Run pipeline with test data + - name: debug-print + if: always() run: | - nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.profile }},docker --outdir ./results + echo "toJSON(needs) = ${{ toJSON(needs) }}" + echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" \ No newline at end of file diff --git a/.gitignore b/.gitignore index 4109b5c9..6f1addc9 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,4 @@ testing/ testing* *.pyc execution_trace* +.nf-test* diff --git a/nf-test.config b/nf-test.config new file mode 100644 index 00000000..867e3fb1 --- /dev/null +++ b/nf-test.config @@ -0,0 +1,16 @@ +config { + // location for all nf-tests + testsDir "tests" + + // nf-test directory including temporary files for each test + workDir ".nf-test" + + // location of library folder that is added automatically to the classpath + libDir "tests/pipeline/lib/" + + // location of an optional nextflow.config file specific for executing tests + configFile "nextflow.config" + + // run all test with the defined docker profile from the main nextflow.config + profile "docker" +} \ No newline at end of file diff --git a/tests/lib/UTILS.groovy b/tests/lib/UTILS.groovy new file mode 100644 index 00000000..deacb586 --- /dev/null +++ b/tests/lib/UTILS.groovy @@ -0,0 +1,11 @@ +// Function to remove Nextflow version from software_versions.yml + +class UTILS { + public static String removeNextflowVersion(outputDir) { + def softwareVersions = path("$outputDir/pipeline_info/nf_core_pipeline_software_mqc_versions.yml").yaml + if (softwareVersions.containsKey("Workflow")) { + softwareVersions.Workflow.remove("Nextflow") + } + return softwareVersions + } +} diff --git a/tests/test.nf.test b/tests/test.nf.test new file mode 100644 index 00000000..6d768fa9 --- /dev/null +++ b/tests/test.nf.test @@ -0,0 +1,263 @@ +nextflow_pipeline { + + name "Test Workflow main.nf - test" + script "main.nf" + profile "test" + tag "test" + tag "pipeline" + + test("test") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert workflow.trace.succeeded().size() == 196 }, + { assert snapshot( + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/mirtop/mirtop.gff"), + path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt") + ).match("mirna_quant") }, + { assert snapshot( + path("$outputDir/bowtie_index/genome/genome.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.3.ebwt"), + path("$outputDir/bowtie_index/genome/genome.edited.fa"), + path("$outputDir/bowtie_index/genome/genome.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt") + ).match("bowtie_index") }, + { assert snapshot( + path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip") + ).match("fastqc") }, + { assert snapshot( + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") + ).match("mirtrace") }, + { assert snapshot( + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.flagstat") + ).match("genome_quant") }, + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_contamination.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_length.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtop.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_complexity.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_samtools_stats.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_fastqc_1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_fastp.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_summary.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt") + ).match("multiqc") }, + ) + } + + } + +} diff --git a/tests/test_index.nf.test b/tests/test_index.nf.test new file mode 100644 index 00000000..56ca7d42 --- /dev/null +++ b/tests/test_index.nf.test @@ -0,0 +1,229 @@ +nextflow_pipeline { + + name "Test Workflow main.nf - test_index" + script "main.nf" + profile "test_index" + tag "test_index" + tag "pipeline" + + test("test_index") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert workflow.trace.succeeded().size() == 161 }, + { assert snapshot( + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop.gff"), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt") + ).match("mirna_quant") }, + { assert snapshot( + path("$outputDir/untar/bowtie_index/genome.1.ebwt"), + path("$outputDir/untar/bowtie_index/genome.rev.1.ebwt"), + path("$outputDir/untar/bowtie_index/genome.4.ebwt"), + path("$outputDir/untar/bowtie_index/genome.3.ebwt"), + path("$outputDir/untar/bowtie_index/genome.rev.2.ebwt"), + path("$outputDir/untar/bowtie_index/genome.2.ebwt") + ).match("untar") }, + { assert snapshot( + path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip") + ).match("fastqc") }, + { assert snapshot( + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") + ).match("mirtrace") }, + { assert snapshot( + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt") + ).match("bowtie_index") }, + { assert snapshot( + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats") + ).match("genome_quant") }, + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_contamination.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_length.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtop.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_complexity.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_samtools_stats.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_fastqc_1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_fastp.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_summary.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt") + ).match("multiqc") }, + ) + } + + } + +} diff --git a/tests/test_no_genome.nf.test b/tests/test_no_genome.nf.test new file mode 100644 index 00000000..3fbb6cd7 --- /dev/null +++ b/tests/test_no_genome.nf.test @@ -0,0 +1,262 @@ +nextflow_pipeline { + + name "Test Workflow main.nf - test_no_genome" + script "main.nf" + profile "test_no_genome" + tag "test_no_genome" + tag "pipeline" + + test("test_no_genome") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert workflow.trace.succeeded().size() == 147 }, + { assert snapshot( + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/Control_N2_seqcluster.bam"), + path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N3_seqcluster.bam"), + path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N1_seqcluster.bam"), + path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N3_seqcluster.bam"), + path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N2_seqcluster.bam"), + path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N1_seqcluster.bam"), + path("$outputDir/mirna_quant/bam/seqcluster/Control_N1_seqcluster.bam"), + path("$outputDir/mirna_quant/bam/seqcluster/Control_N3_seqcluster.bam"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N2_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N3_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N1_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N3_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N2_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N1_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N1_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N3_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N2_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N3_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone1_N3_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N1_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N2_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone1_N1_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N1_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N3_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N2_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N3_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N3_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N2_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N1_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N1_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N1_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N3_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop.gff"), + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt") + ).match("mirna_quant") }, + { assert snapshot( + path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip") + ).match("fastqc") }, + { assert snapshot( + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta") + ).match("mirtrace") }, + { assert snapshot( + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt") + ).match("bowtie_index") }, + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_contamination.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_length.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtop.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_complexity.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_samtools_stats.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_fastqc_1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_fastp.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_summary.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt") + ).match("multiqc") }, + ) + } + + } + +} diff --git a/tests/test_umi.nf.test b/tests/test_umi.nf.test new file mode 100644 index 00000000..72a3deff --- /dev/null +++ b/tests/test_umi.nf.test @@ -0,0 +1,184 @@ + +nextflow_pipeline { + + name "Test Workflow main.nf - test_umi" + script "main.nf" + profile "test_umi" + tag "test_umi" + tag "pipeline" + + test("test_umi") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert workflow.trace.succeeded().size() == 64 }, + { assert snapshot( + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195118_SRR11631014_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195117_SRR11631013_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/SRX8195118_SRR11631014_seqcluster.bam"), + path("$outputDir/mirna_quant/bam/seqcluster/SRX8195117_SRR11631013_seqcluster.bam"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195118_SRR11631014_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195117_SRR11631013_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/SRX8195118_SRR11631014_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/SRX8195117_SRR11631013_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/SRX8195118_SRR11631014.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/SRX8195117_SRR11631013.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop.gff"), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt") + ).match("mirna_quant") }, + { assert snapshot( + path("$outputDir/bowtie_index/genome/genome.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.3.ebwt"), + path("$outputDir/bowtie_index/genome/genome.4.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.edited.fa"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt") + ).match("bowtie_index") }, + { assert snapshot( + path("$outputDir/fastqc/raw/SRX8195118_SRR11631014.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/SRX8195117_SRR11631013.raw_fastqc.zip"), + path("$outputDir/fastqc/trimmed/SRX8195118_SRR11631014.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/SRX8195117_SRR11631013.trim_fastqc.zip") + ).match("fastqc") }, + { assert snapshot( + path("$outputDir/umi_dedup/bam_deduplicated/SRX8195118_SRR11631014.umi_dedup.sorted.fastq.gz"), + path("$outputDir/umi_dedup/bam_deduplicated/SRX8195117_SRR11631013.umi_dedup.sorted.fastq.gz"), + path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195118_SRR11631014.umi_extract.fastq.gz"), + path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195117_SRR11631013.umi_extract.fastq.gz") + ).match("umi_dedup") }, + { assert snapshot( + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/SRX8195118_SRR11631014.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/SRX8195117_SRR11631013.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/SRX8195118_SRR11631014.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/SRX8195117_SRR11631013.fastp.fasta") + ).match("mirtrace") }, + { assert snapshot( + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats") + ).match("genome_quant") }, + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), + path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_contamination_check_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt") + ).match("multiqc") }, + ) + } + + } + +} From a574696f07cf723f218e12f6240f8420053f39cc Mon Sep 17 00:00:00 2001 From: zxBIB Schcolnicov Date: Mon, 19 Aug 2024 19:31:33 +0200 Subject: [PATCH 02/15] Added techincalrepeats nftest and updated nf-test config --- nf-test.config | 5 +- tests/test_technical_repeats.nf.test | 140 +++++++++++++++++++++++++++ 2 files changed, 141 insertions(+), 4 deletions(-) create mode 100644 tests/test_technical_repeats.nf.test diff --git a/nf-test.config b/nf-test.config index 867e3fb1..ce896ed3 100644 --- a/nf-test.config +++ b/nf-test.config @@ -6,11 +6,8 @@ config { workDir ".nf-test" // location of library folder that is added automatically to the classpath - libDir "tests/pipeline/lib/" + libDir "tests/lib/" // location of an optional nextflow.config file specific for executing tests configFile "nextflow.config" - - // run all test with the defined docker profile from the main nextflow.config - profile "docker" } \ No newline at end of file diff --git a/tests/test_technical_repeats.nf.test b/tests/test_technical_repeats.nf.test new file mode 100644 index 00000000..4d7659e2 --- /dev/null +++ b/tests/test_technical_repeats.nf.test @@ -0,0 +1,140 @@ +nextflow_pipeline { + + name "Test Workflow main.nf - test_technical_repeats" + script "main.nf" + profile "test_technical_repeats" + tag "test_technical_repeats" + tag "pipeline" + + test("test_technical_repeats") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert workflow.trace.succeeded().size() == 75 }, + { assert snapshot( + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop.gff"), + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt") + ).match("mirna_quant") }, + { assert snapshot( + path("$outputDir/bowtie_index/genome/genome.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.4.ebwt"), + path("$outputDir/bowtie_index/genome/genome.3.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.edited.fa"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt") + ).match("bowtie_index") }, + { assert snapshot( + path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") + ).match("mirtrace") }, + { assert snapshot( + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats") + ).match("genome_quant") }, + ) + } + + } + +} From 70a62c608fe3e1c894c37211bb47303154b97fc6 Mon Sep 17 00:00:00 2001 From: zxBIB Schcolnicov Date: Mon, 19 Aug 2024 22:39:32 +0200 Subject: [PATCH 03/15] Updated tests and added snaps --- tests/test.nf.test | 408 ++++++++++++---------- tests/test.nf.test.snap | 319 +++++++++++++++++ tests/test_index.nf.test | 347 ++++++++++-------- tests/test_index.nf.test.snap | 292 ++++++++++++++++ tests/test_no_genome.nf.test | 401 +++++++++++---------- tests/test_no_genome.nf.test.snap | 311 +++++++++++++++++ tests/test_technical_repeats.nf.test | 171 ++++----- tests/test_technical_repeats.nf.test.snap | 153 ++++++++ tests/test_umi.nf.test | 265 +++++++------- tests/test_umi.nf.test.snap | 217 ++++++++++++ 10 files changed, 2148 insertions(+), 736 deletions(-) create mode 100644 tests/test.nf.test.snap create mode 100644 tests/test_index.nf.test.snap create mode 100644 tests/test_no_genome.nf.test.snap create mode 100644 tests/test_technical_repeats.nf.test.snap create mode 100644 tests/test_umi.nf.test.snap diff --git a/tests/test.nf.test b/tests/test.nf.test index 6d768fa9..098e74d5 100644 --- a/tests/test.nf.test +++ b/tests/test.nf.test @@ -10,7 +10,7 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } } @@ -19,166 +19,258 @@ nextflow_pipeline { { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, { assert workflow.trace.succeeded().size() == 196 }, + { assert snapshot( - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), + path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.edited.fa"), + path("$outputDir/bowtie_index/genome/genome.3.ebwt"), + path("$outputDir/bowtie_index/genome/genome.4.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") + ).match("bowtie_index") }, + + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), + path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") + ).match("multiqc") }, + + { assert snapshot( + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai") + ).match("genome_quant") }, + + { assert snapshot( + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/mirtop/mirtop.gff"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop.gff"), path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt") + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") ).match("mirna_quant") }, + { assert snapshot( - path("$outputDir/bowtie_index/genome/genome.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.3.ebwt"), - path("$outputDir/bowtie_index/genome/genome.edited.fa"), - path("$outputDir/bowtie_index/genome/genome.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt") - ).match("bowtie_index") }, - { assert snapshot( - path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip"), path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip"), path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip"), path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip"), path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip"), path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip"), path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip") + path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip") ).match("fastqc") }, + { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), @@ -198,63 +290,7 @@ nextflow_pipeline { path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") ).match("mirtrace") }, - { assert snapshot( - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.flagstat") - ).match("genome_quant") }, - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_contamination.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_length.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtop.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_complexity.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_samtools_stats.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_fastqc_1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_fastp.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_summary.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt") - ).match("multiqc") }, + ) } diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap new file mode 100644 index 00000000..b26b2a15 --- /dev/null +++ b/tests/test.nf.test.snap @@ -0,0 +1,319 @@ +{ + "bowtie_index": { + "content": [ + "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", + "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", + "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", + "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", + "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", + "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", + "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", + "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", + "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", + "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", + "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", + "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", + "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", + "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", + "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", + "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", + "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", + "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", + "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:05:11.173010609" + }, + "mirtrace": { + "content": [ + "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", + "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", + "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", + "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", + "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", + "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", + "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638", + "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", + "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", + "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", + "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", + "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", + "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", + "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", + "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8", + "Clone1_N1.fastp.fasta:md5,e297dfa46353946d6c140e4513dd4525", + "Clone9_N1.fastp.fasta:md5,63a17d136548fc98f34c8d98006cc7da", + "Control_N3.fastp.fasta:md5,d9980a598ece252e19d6c9ebefd51861", + "Control_N1.fastp.fasta:md5,e964e05ce2c93937a8e76602f2e08150", + "Clone9_N2.fastp.fasta:md5,b1ca39e6e1e75ee7d654d9ccfb35e906", + "Control_N2.fastp.fasta:md5,8cefbc494be7b363b19c10b8c00366b2", + "Clone1_N3.fastp.fasta:md5,4012282462dde0750f09cec883304cc3", + "Clone9_N3.fastp.fasta:md5,f733e20eb8d2a2009ca82464e8ccb148" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:05:41.566106027" + }, + "genome_quant": { + "content": [ + "Clone9_N2_mature_hairpin_genome.sorted.flagstat:md5,b8fbbdaca0458b19732312dea2997be8", + "Control_N1_mature_hairpin_genome.sorted.flagstat:md5,18f0028f1cfc137ef8f089e465fe20f5", + "Control_N2_mature_hairpin_genome.sorted.flagstat:md5,b0d42e94b2e0e026cd32a88dce40722c", + "Control_N3_mature_hairpin_genome.sorted.stats:md5,53e8fca566dd5dd8553b25c38e961f6b", + "Clone1_N3_mature_hairpin_genome.sorted.stats:md5,fb089da3351a3f8c0bc742f3f4533349", + "Clone9_N3_mature_hairpin_genome.sorted.stats:md5,8ec73033ee0e2ad16fdc497b209adb50", + "Clone9_N3_mature_hairpin_genome.sorted.flagstat:md5,dbe38679a68d55b8a182831e336eebb1", + "Clone9_N1_mature_hairpin_genome.sorted.bam:md5,7acf27a7533fbec27aa270637a919bed", + "Clone1_N1_mature_hairpin_genome.sorted.flagstat:md5,4d552770e6d3b06775b6f484684f7a77", + "Control_N2_mature_hairpin_genome.sorted.stats:md5,f105861208044e44644c74449d0c6142", + "Control_N2_mature_hairpin_genome.sorted.idxstats:md5,b6da32ce230fdeab39f3c4d5dcf41a3a", + "Clone1_N1_mature_hairpin_genome.sorted.bam:md5,1a438500002e75f6bf8cca6fe191b580", + "Control_N2_mature_hairpin_genome.sorted.bam.bai:md5,9b5d9073c4ffad7f128249ba2fef8b5c", + "Clone1_N1_mature_hairpin_genome.sorted.bam.bai:md5,0dfb96ad1d7201c0684c92b6caf4883e", + "Clone1_N3_mature_hairpin_genome.sorted.idxstats:md5,d680e48370d319f1891cdd61b8754644", + "Clone9_N3_mature_hairpin_genome.sorted.bam:md5,0427bf26d0a19a9f67c849ced65d7236", + "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,64b19984a4c2fa55e69a28fe7c138d7c", + "Control_N3_mature_hairpin_genome.sorted.bam.bai:md5,aab8b4709b5bcab35fe8b4b68a2f8550", + "Clone9_N2_mature_hairpin_genome.sorted.bam:md5,85456566c2745be254fee1bc633c503b", + "Control_N1_mature_hairpin_genome.sorted.bam:md5,c6ab347e1b3bba44b66da20fda537fe3", + "Control_N3_mature_hairpin_genome.sorted.flagstat:md5,ae834e3dbaa18aa9bce66c3b0034c430", + "Clone9_N1_mature_hairpin_genome.sorted.idxstats:md5,a199f8999ba915a81acfc450e0db8393", + "Control_N3_mature_hairpin_genome.sorted.bam:md5,68be42f8696b4ef53d917706fa73b183", + "Control_N1_mature_hairpin_genome.sorted.idxstats:md5,fe01b41ed88612c28b667817c4a8fcc1", + "Clone1_N3_mature_hairpin_genome.sorted.bam:md5,fee1f04d814e3b20a33322487a2165e6", + "Clone9_N1_mature_hairpin_genome.sorted.bam.bai:md5,73e9d2c87726c85b18bb622e43b9d716", + "Clone1_N3_mature_hairpin_genome.sorted.flagstat:md5,9dee041c82ad3b2d2ab4f8986822f2ce", + "Control_N2_mature_hairpin_genome.sorted.bam:md5,b1a91d8754d5a480ec9d05f93d9f3025", + "Control_N1_mature_hairpin_genome.sorted.stats:md5,b2afcfcb9e785a71bb5fce25b87fd67a", + "Clone9_N2_mature_hairpin_genome.sorted.bam.bai:md5,a66453d898f5cb49fc945b0f8cfe5ff3", + "Control_N3_mature_hairpin_genome.sorted.idxstats:md5,94d53c9ad335779a1ea25fd5b4b08069", + "Control_N1_mature_hairpin_genome.sorted.bam.bai:md5,915c6a1d11d7f69ef575f79dc3a08aa0", + "Clone9_N2_mature_hairpin_genome.sorted.stats:md5,6db5d451fa95a77247d38c4a263cf05d", + "Clone9_N1_mature_hairpin_genome.sorted.stats:md5,f819db926f570a9bb1cf9b6adff7d758", + "Clone9_N3_mature_hairpin_genome.sorted.idxstats:md5,0a227abfa6aa10023219bce7b2795b67", + "Clone9_N1_mature_hairpin_genome.sorted.flagstat:md5,2fd8cd41edde2292f857528658c3e0a1", + "Clone9_N2_mature_hairpin_genome.sorted.idxstats:md5,61c4821cba66c91272e62547617db2c9", + "Clone1_N3_mature_hairpin_genome.sorted.bam.bai:md5,667b65be13c5b4984f15f402e84d2949", + "Clone1_N1_mature_hairpin_genome.sorted.idxstats:md5,169a196ee2da6945392f6a361164ffc5", + "Clone9_N3_mature_hairpin_genome.sorted.bam.bai:md5,c8b6df11a72663b9ca445847b6ae7112" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:05:11.797960575" + }, + "software_versions": { + "content": [ + "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_GENOME={bowtie=1.3.1}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:05:11.154500508" + }, + "fastqc": { + "content": [ + "Control_N1.raw_fastqc.zip:md5,4945e02703cd784c0ba587f371bd6f67", + "Clone9_N3.raw_fastqc.zip:md5,c6713743bb347f82dacabadfe9b1852e", + "Clone9_N1.raw_fastqc.zip:md5,f73e5b9915222ed05297bedbb51221e3", + "Control_N3.raw_fastqc.zip:md5,cbf237bc37344817bc720c840ed64c17", + "Clone1_N3.raw_fastqc.zip:md5,d58dce4bd438620a01bbb6a101ed2d5d", + "Control_N2.raw_fastqc.zip:md5,2a470a5c426dfdd8fcc869e243d77267", + "Clone9_N2.raw_fastqc.zip:md5,334b6c0a58619499cc4bcbc1421cd929", + "Clone1_N1.raw_fastqc.zip:md5,ee48e5fd1f87377d1d69b8a7f1cd23cc", + "Control_N3.trim_fastqc.zip:md5,b30a77afece684d59a16711cbd20744f", + "Clone9_N3.trim_fastqc.zip:md5,904abad8ce0fdaf6160f0f1fd7a66726", + "Clone9_N2.trim_fastqc.zip:md5,649b56c3dd1310e8a8fceaf8e3382c35", + "Clone9_N1.trim_fastqc.zip:md5,982945e7e8e052394772ad894fdcb402", + "Clone1_N1.trim_fastqc.zip:md5,d0d0f3d0c7bea925a9e7f4169ed4f44e", + "Control_N2.trim_fastqc.zip:md5,2e8dcbe9c8d87a533268cc40aa8ce6c7", + "Control_N1.trim_fastqc.zip:md5,628ac81e0ad2b4852a2a0048fcc7c268", + "Clone1_N3.trim_fastqc.zip:md5,1275f55e2d3c20b04d2a37bd36184d00" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:05:28.698286359" + }, + "multiqc": { + "content": [ + "fastqc-status-check-heatmap.txt:md5,30f55902420433a11971d36956e8576e", + "fastp_filtered_reads_plot.txt:md5,0af4d3cfbf463f33b2b88cdfd69909ac", + "fastqc_overrepresented_sequences_plot.txt:md5,d861a4a956a3023efa19b1259d8665b2", + "fastqc_top_overrepresented_sequences_table-1.txt:md5,f214e5c6c2e16e9fc0721e3299aa6af7", + "fastqc_sequence_counts_plot-1.txt:md5,37d8ae6c5734eb2679e65e46c9af9101", + "mirtrace_complexity_plot.txt:md5,5f78d6f559a9642e68e1fd74ac2c11ca", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", + "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", + "samtools-stats-dp.txt:md5,61a77aab820a3eba21a51e32168b45e3", + "fastqc_sequence_length_distribution_plot.txt:md5,13f72b3be854c74cd7b5176ca0583770", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "fastqc_sequence_duplication_levels_plot-1.txt:md5,06a4162d4787883b1f39a1b9acb7bb91", + "fastqc_per_base_sequence_quality_plot-1.txt:md5,6a0df664a369ee216412f0033ed3a042", + "multiqc_general_stats.txt:md5,b4693299615f59864df56a7279bf1bc5", + "fastqc_per_base_n_content_plot-1.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "fastqc_per_base_n_content_plot.txt:md5,fb8a49467d1679dbf716e1f00c1f25e5", + "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,b1481a9fbf5ea541b39aed99b51d616f", + "fastqc_per_sequence_quality_scores_plot.txt:md5,38dbd6509de7f1beac17e44acb8336be", + "mirtrace_qc_plot.txt:md5,c436d017382baed6617fc3c1ad8ab41d", + "fastqc_per_sequence_quality_scores_plot-1.txt:md5,69f4459318311103fe71a5d1d3b2c076", + "mirtrace_length_plot.txt:md5,2366f10eb8bd3c32d2b35e2df20c786c", + "fastqc_top_overrepresented_sequences_table.txt:md5,9acec391e0a46858e110f5baa65fb0a9", + "fastqc_overrepresented_sequences_plot-1.txt:md5,1de000de50cc7516bb9d996def14c6eb", + "fastqc-status-check-heatmap-1.txt:md5,e64c353797e6dc057d10b3194ca6b20d", + "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", + "mirtrace_rna_categories_plot.txt:md5,8665376e2a123e1661f82cbbee54789f", + "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", + "samtools_alignment_plot.txt:md5,f87f3d2101f70e840c57df850bd1e3be", + "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", + "mirtop_read_count_plot.txt:md5,29cce56b45edc10ff63badfa49eaf6b9", + "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "mirtop_unique_read_count_plot.txt:md5,b540743844ef0cdb81390b9db1d23afe", + "mirtop_mean_read_count_plot.txt:md5,837e240c5ecd10b95257e65fcd9f8393", + "fastqc_adapter_content_plot.txt:md5,86a0f478fd3e690ef5132d08bf4e7625", + "fastqc_sequence_duplication_levels_plot.txt:md5,88b0babe77f623547e8af664791ef2d0", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,539883757ae5bf731da93fe0568022e9", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,ed7205b9c46d5f431c5b3bf499a673a1", + "fastqc_adapter_content_plot-1.txt:md5,71ba0983a71f3a833526ab83a985d072", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,a8387a3e6b350acd16bb0ed5a43949d8", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3e9c1a7204c12d9c1b3b53342cf61840", + "multiqc_sources.txt:md5,ff2a4d4e1142cf341d6d14ae56dca6e8", + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,efa8123c9ad43f99a6fba671f50322ca" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:05:11.501195707" + }, + "mirna_quant": { + "content": [ + "Control_N1_mature_hairpin.sorted.stats:md5,feb69ad2f8bbc527e39502a297f08abd", + "Control_N1_mature_hairpin.sorted.idxstats:md5,e1f455195f1cb42a1d1e58770aaeb2b4", + "Clone1_N3_mature_hairpin.sorted.flagstat:md5,6f14ec4cd502c0eb213b1905b4568a76", + "Clone9_N2_mature_hairpin.sorted.stats:md5,7bb8654d44dac245aec6aa045250628a", + "Clone9_N3_mature_hairpin.sorted.flagstat:md5,efc65cb620ca139b19967e12f13ba007", + "Control_N1_mature_hairpin.sorted.bam.bai:md5,38248e27a6928359b3ffb2cd38accfeb", + "Control_N3_mature_hairpin.sorted.bam.bai:md5,2517024b6a616d267528e3ca9d1fc48d", + "Control_N1_mature_hairpin.sorted.flagstat:md5,41769a400a176ea78432749f07f80fda", + "Control_N1_mature_hairpin.sorted.bam:md5,0eab30f74fc0bd6d14ccd70a277a9746", + "Clone9_N1_mature_hairpin.sorted.stats:md5,155f327a9be0afa9584ec426826b5457", + "Clone1_N3_mature_hairpin.sorted.bam:md5,b6db05f1752865f1f41a87b42b1344e1", + "Control_N2_mature_hairpin.sorted.stats:md5,1195dd51f77e338db83dc66476ac7c5f", + "Clone9_N1_mature_hairpin.sorted.bam.bai:md5,c8e5fd0e315417c7bfc741fb3f9482e0", + "Control_N3_mature_hairpin.sorted.idxstats:md5,2c44710ce63bdebb12d64c729ef338b0", + "Control_N2_mature_hairpin.sorted.bam.bai:md5,fc6c5ea2d38928afad19a85ea7b51b47", + "Clone1_N3_mature_hairpin.sorted.bam.bai:md5,d1114e75e59ba3a957612b3d59b77675", + "Clone1_N1_mature_hairpin.sorted.idxstats:md5,0bca2d01f734128f3c11cf2697433048", + "Clone9_N3_mature_hairpin.sorted.idxstats:md5,9523d29d411c2efb0a1756355230fa98", + "Control_N2_mature_hairpin.sorted.idxstats:md5,8859b6e432cef8b24d5fb258a06aaabe", + "Clone9_N2_mature_hairpin.sorted.flagstat:md5,663ae0bb8b29d1e1c3d75ef5df1015a4", + "Clone9_N1_mature_hairpin.sorted.flagstat:md5,3e4b295b54df05c438603edaa53123b1", + "Control_N3_mature_hairpin.sorted.flagstat:md5,f3df866b94dc6ef355b01f22047aaf4f", + "Clone1_N1_mature_hairpin.sorted.bam.bai:md5,5ee1751e41db25b7f2f110f58bbf7265", + "Clone1_N1_mature_hairpin.sorted.bam:md5,90241892e182624a3a9723f1067d62bd", + "Control_N3_mature_hairpin.sorted.bam:md5,c57b368d688cf84a120a111652fe21a6", + "Clone9_N3_mature_hairpin.sorted.stats:md5,9f61c028bb1c92667e31093156ada662", + "Clone1_N1_mature_hairpin.sorted.stats:md5,bd02cb15e666054edecc89d392d72902", + "Clone9_N2_mature_hairpin.sorted.idxstats:md5,04b1c0ea4f133b5ee9086eec1f4077e7", + "Clone1_N3_mature_hairpin.sorted.stats:md5,471db325d8ccd1fe787b5dd91dccf487", + "Clone9_N3_mature_hairpin.sorted.bam.bai:md5,b10a95e003f8af2a0926ab38b0bcef61", + "Control_N2_mature_hairpin.sorted.flagstat:md5,2605548b5ab1e6ad6b5cf88ea0030909", + "Clone9_N1_mature_hairpin.sorted.idxstats:md5,238b462a2418d545418c0b3a28029bdf", + "Clone9_N2_mature_hairpin.sorted.bam.bai:md5,3566fc7328df89c8a2ed3b6dfcc60347", + "Control_N3_mature_hairpin.sorted.stats:md5,2f2249c537451d1f72dfe298f16093ac", + "Clone9_N1_mature_hairpin.sorted.bam:md5,4a8d7da1400e517fa08e196ac1967ecd", + "Clone9_N2_mature_hairpin.sorted.bam:md5,54c118f5f09e088de202bb633ede528b", + "Clone1_N1_mature_hairpin.sorted.flagstat:md5,8d0c785fec7b300200863c68b158444c", + "Control_N2_mature_hairpin.sorted.bam:md5,b03472ce507546b4f703d95a102a3ba4", + "Clone9_N3_mature_hairpin.sorted.bam:md5,0702924e1eef55817b1542e031c66e4d", + "Clone1_N3_mature_hairpin.sorted.idxstats:md5,5b6cd8d5784c387d2649f18499a17c6e", + "Control_N1_mature.sorted.bam.bai:md5,9ad0d0c840f6335ae7227cfdf03f714a", + "Clone1_N1_mature.sorted.stats:md5,9c42ffda181ca24ab076efc16fcfd4b3", + "Clone1_N3_mature.sorted.idxstats:md5,805f115ac4d9c8033908bafaba6c92fb", + "Clone9_N2_mature.sorted.stats:md5,fb8c403012481dafb895013c555f6d85", + "Control_N2_mature.sorted.stats:md5,ef5935898e3ca45d898053af335d1dfb", + "Control_N3_mature.sorted.flagstat:md5,2831f55bccbcf666d1c313ef377bcb30", + "Clone9_N3_mature.sorted.bam:md5,326a16bafc12f91277d43718612784a7", + "Clone9_N1_mature.sorted.bam.bai:md5,0d1a7dbe6e97f7fa4811790e6640c978", + "Clone9_N3_mature.sorted.stats:md5,23b012dd60ea6dcec5cedb5a73ffc792", + "Clone1_N1_mature.sorted.bam:md5,216cd7ea3aef9cdb3dc58f5a273ac995", + "Clone1_N3_mature.sorted.flagstat:md5,67fc6ba8516d4e5b3ed2a62febc92f0a", + "Clone9_N1_mature.sorted.idxstats:md5,c6eb22f3ff675e422d065375279150b2", + "Control_N1_mature.sorted.bam:md5,dde5afbe3b7b28da315eefafe279a9b8", + "Control_N1_mature.sorted.stats:md5,b4ffb3a7623e32420def4d3470a326ab", + "Control_N1_mature.sorted.idxstats:md5,847bc5c6ef44e1f9754e47e648a5ef98", + "Clone9_N2_mature.sorted.flagstat:md5,247e02da50509fc1b3c5b35001922a8d", + "Control_N2_mature.sorted.flagstat:md5,c8742d1b49535ff815c2def66cba681e", + "Control_N2_mature.sorted.bam.bai:md5,01e9905b9d121d3c0341488bade69180", + "Control_N2_mature.sorted.bam:md5,52b89aab08865d6639269583fc1a42ac", + "Clone9_N2_mature.sorted.bam.bai:md5,a68809526ec55ae96f6eb62a170ac5ca", + "Control_N2_mature.sorted.idxstats:md5,12388de965d69b6102b62bc9cdf27e85", + "Control_N3_mature.sorted.bam.bai:md5,720f79c56ab38ba1ebafeb9c0fe5cf45", + "Clone9_N1_mature.sorted.flagstat:md5,014b846757652783ff3f954a966b8a1b", + "Clone9_N2_mature.sorted.bam:md5,8250cb44af17d1ccee889f14b41e5da1", + "Clone1_N3_mature.sorted.bam.bai:md5,567e08c765069502219a2bf080a84600", + "Clone9_N3_mature.sorted.idxstats:md5,dee54e8e22dfca24acc290bf89a05cd4", + "Clone9_N2_mature.sorted.idxstats:md5,c9643d610de2f4d449a876e41dcab872", + "Clone9_N3_mature.sorted.flagstat:md5,4f60cfd3527e91df204253f9f1aebfcd", + "Control_N3_mature.sorted.idxstats:md5,5fb7b46915043bd3c947a37afc3e8075", + "Clone9_N3_mature.sorted.bam.bai:md5,b1ac22e2ceb13f78bcede9cef82d2989", + "Clone1_N1_mature.sorted.bam.bai:md5,6b5783e42dca72415ed9cc25cd94b6cb", + "Clone1_N1_mature.sorted.idxstats:md5,77ed64ddd23cf07340b65c04559d4726", + "Control_N3_mature.sorted.bam:md5,9016fcda58013dedb5dea875cc718bd8", + "Clone1_N1_mature.sorted.flagstat:md5,f138a532bc7dab94f7cf4b4a4e5e23e5", + "Control_N3_mature.sorted.stats:md5,ff9dab4d3220aa44cdc80ea2fc311823", + "Clone1_N3_mature.sorted.stats:md5,e8feced949af44c8e5d31523b12122b9", + "Clone1_N3_mature.sorted.bam:md5,ffa1485c08ac5f4a2edebb88c892a7d6", + "Clone9_N1_mature.sorted.bam:md5,9fc8f4311a10f8ed65151017d861ab7f", + "Control_N1_mature.sorted.flagstat:md5,16318a574fe410b81c0e2cdf0dfa3c97", + "Clone9_N1_mature.sorted.stats:md5,02184884c17c8730f4df9e1a6144bbdc", + "mirna.tsv:md5,1f840afe7ab68eac73feaaad321b64f6", + "mirtop.tsv:md5,671628c0cf82376f674562ba1a6f6790", + "mirtop.gff:md5,598d14684b224dc897e3324448da2a7d", + "mirtop_rawData.tsv:md5,774410dd2cf1e5be83bf8d6e1e8b96b0", + "mirtop_stats.txt:md5,8b1ce9988d872c72ab3b23ed43000f7c", + "Clone1_N3.fastp_trimmed.fastq.gz:md5,2e395240c74b3870efe03dc329d8bad8", + "Control_N1.fastp_trimmed.fastq.gz:md5,2f09082eb68a8f1dc308050e330887ec", + "Control_N3.fastp_trimmed.fastq.gz:md5,342368a6e6acdaf0ae9379676b6d07f0", + "Clone9_N1.fastp_trimmed.fastq.gz:md5,115cf0c346a93a47ba782c5724b4f090", + "Clone1_N1.fastp_trimmed.fastq.gz:md5,14a2590e663dbde105780726c2173c25", + "Clone9_N2.fastp_trimmed.fastq.gz:md5,c922ec95a4b84d806dd2054ff0f9cab7", + "Clone9_N3.fastp_trimmed.fastq.gz:md5,67cf9a7d2fa431f0e772391ed1651f93", + "Control_N2.fastp_trimmed.fastq.gz:md5,d6e607edcb3d71c546ce8fdfb18e3999", + "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", + "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", + "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "mature_unmapped_read_counts.txt:md5,5673c4e9f6715d7ae7e137035e7e080e", + "mature_normalized_CPM.txt:md5,f6d11da1bb701b19780093094421c10e", + "hairpin_logtpm.csv:md5,923c8fff7480c89bcb18acfa2b398b4a", + "mature_logtpm.txt:md5,8851354ac087c8547aa9710eb49bc1d5", + "mature_edgeR_MDS_plot_coordinates.txt:md5,dfca9dca59af62be59bf43a10c9ee27e", + "hairpin_unmapped_read_counts.txt:md5,432fb18356e27c15569b62140f482435", + "mature_edgeR_MDS_distance_matrix.txt:md5,d386896da5ba156a76052895253f41c5", + "mature_log2CPM_sample_distances.txt:md5,bea4b11907cd6badbc68e9b505a48bb8", + "hairpin_log2CPM_sample_distances.txt:md5,b19fa1d9f821fc8e2c0e9f34f76b5479", + "hairpin_edgeR_MDS_distance_matrix.txt:md5,71074c2cb4661feaf822929250c8d3a9", + "hairpin_logtpm.txt:md5,d474bafadfed004173d15094ff6d4e25", + "hairpin_edgeR_MDS_plot_coordinates.txt:md5,666f384ea6cdd06a6140b8b9c8e2bb66", + "mature_logtpm.csv:md5,2ecf0babb4dfed8f25be9a40b953855d", + "hairpin_normalized_CPM.txt:md5,1c1104bda88b19465e890e8f7fdbac86", + "mature_counts.csv:md5,c006871cb0a4b01c47de2c0d8955fd0a", + "hairpin_counts.csv:md5,64d35f8b6fa3dfac237d944c1463cd03" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:05:15.071197394" + } +} \ No newline at end of file diff --git a/tests/test_index.nf.test b/tests/test_index.nf.test index 56ca7d42..86e6b2f9 100644 --- a/tests/test_index.nf.test +++ b/tests/test_index.nf.test @@ -10,7 +10,7 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } } @@ -19,155 +19,227 @@ nextflow_pipeline { { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, { assert workflow.trace.succeeded().size() == 161 }, + { assert snapshot( - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") + ).match("bowtie_index") }, + + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), + path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") + ).match("multiqc") }, + + { assert snapshot( + path("$outputDir/untar/bowtie_index/genome.rev.2.ebwt"), + path("$outputDir/untar/bowtie_index/genome.2.ebwt"), + path("$outputDir/untar/bowtie_index/genome.1.ebwt"), + path("$outputDir/untar/bowtie_index/genome.3.ebwt"), + path("$outputDir/untar/bowtie_index/genome.4.ebwt"), + path("$outputDir/untar/bowtie_index/genome.rev.1.ebwt") + ).match("untar") }, + + { assert snapshot( + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam") + ).match("genome_quant") }, + + { assert snapshot( + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), path("$outputDir/mirna_quant/mirtop/mirtop.gff"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt") + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") ).match("mirna_quant") }, + { assert snapshot( - path("$outputDir/untar/bowtie_index/genome.1.ebwt"), - path("$outputDir/untar/bowtie_index/genome.rev.1.ebwt"), - path("$outputDir/untar/bowtie_index/genome.4.ebwt"), - path("$outputDir/untar/bowtie_index/genome.3.ebwt"), - path("$outputDir/untar/bowtie_index/genome.rev.2.ebwt"), - path("$outputDir/untar/bowtie_index/genome.2.ebwt") - ).match("untar") }, - { assert snapshot( + path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip"), path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip"), path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip"), path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip"), path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip") + path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip") ).match("fastqc") }, + { assert snapshot( path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), @@ -185,42 +257,7 @@ nextflow_pipeline { path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") ).match("mirtrace") }, - { assert snapshot( - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt") - ).match("bowtie_index") }, - { assert snapshot( - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats") - ).match("genome_quant") }, - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_contamination.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_length.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtop.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_complexity.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_samtools_stats.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_fastqc_1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_fastp.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_summary.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt") - ).match("multiqc") }, + ) } diff --git a/tests/test_index.nf.test.snap b/tests/test_index.nf.test.snap new file mode 100644 index 00000000..f9fb5e9f --- /dev/null +++ b/tests/test_index.nf.test.snap @@ -0,0 +1,292 @@ +{ + "bowtie_index": { + "content": [ + "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", + "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", + "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", + "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", + "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", + "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", + "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", + "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", + "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", + "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", + "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", + "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:14:50.023826353" + }, + "mirtrace": { + "content": [ + "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", + "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", + "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", + "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", + "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", + "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", + "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638", + "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", + "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", + "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", + "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", + "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", + "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", + "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", + "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8", + "Clone1_N1.fastp.fasta:md5,e297dfa46353946d6c140e4513dd4525", + "Clone9_N1.fastp.fasta:md5,63a17d136548fc98f34c8d98006cc7da", + "Control_N3.fastp.fasta:md5,d9980a598ece252e19d6c9ebefd51861", + "Control_N1.fastp.fasta:md5,e964e05ce2c93937a8e76602f2e08150", + "Clone9_N2.fastp.fasta:md5,b1ca39e6e1e75ee7d654d9ccfb35e906", + "Control_N2.fastp.fasta:md5,8cefbc494be7b363b19c10b8c00366b2", + "Clone1_N3.fastp.fasta:md5,4012282462dde0750f09cec883304cc3", + "Clone9_N3.fastp.fasta:md5,f733e20eb8d2a2009ca82464e8ccb148" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:15:11.764221931" + }, + "genome_quant": { + "content": [ + "Control_N2_mature_hairpin_genome.sorted.flagstat:md5,b0d42e94b2e0e026cd32a88dce40722c", + "Control_N2_mature_hairpin_genome.sorted.stats:md5,1222b755feaf406ecea3f2abb35a737c", + "Control_N2_mature_hairpin_genome.sorted.idxstats:md5,b6da32ce230fdeab39f3c4d5dcf41a3a", + "Control_N2_mature_hairpin_genome.sorted.bam.bai:md5,4052b95a49716e7f1b7309344bd01e67", + "Control_N2_mature_hairpin_genome.sorted.bam:md5,2dc37926d8badbbe3b88b24430f5be67" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:14:50.578371837" + }, + "software_versions": { + "content": [ + "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, UNTAR_BOWTIE_INDEX={untar=1.3}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:14:50.021513324" + }, + "fastqc": { + "content": [ + "Control_N1.raw_fastqc.zip:md5,81f40570d63474bcf55abda315e29c45", + "Clone9_N3.raw_fastqc.zip:md5,66cb401b11ae6813204606aeccf1b8c8", + "Clone9_N1.raw_fastqc.zip:md5,beeef245ec717610477b16e4641f84c7", + "Control_N3.raw_fastqc.zip:md5,38d38114fc7e4052ff55a2255e368e73", + "Clone1_N3.raw_fastqc.zip:md5,5e92a1505bd3e4fb16da4796121a20fb", + "Control_N2.raw_fastqc.zip:md5,14a252bb4fdd6e77afa93803e0ec55dd", + "Clone9_N2.raw_fastqc.zip:md5,441c1fff9495796fa9ad311ef2783ce0", + "Clone1_N1.raw_fastqc.zip:md5,2289535f7e4ad7e6fe40db782685f7d6", + "Control_N3.trim_fastqc.zip:md5,9d1ced8a86b9d4e4eef152e9108108b2", + "Clone9_N3.trim_fastqc.zip:md5,0395cef983e26ed88323abe68ecc3ab9", + "Clone9_N2.trim_fastqc.zip:md5,66ceb8ea7563c1e7bbcbc8c70049cf2f", + "Clone9_N1.trim_fastqc.zip:md5,ee1f6a9d7998e4ac56fb15d13e39f4d9", + "Clone1_N1.trim_fastqc.zip:md5,d492d242944b2d86790582f4e9a2d724", + "Control_N2.trim_fastqc.zip:md5,47220a78db4a3667190f0702f9ed01a0", + "Control_N1.trim_fastqc.zip:md5,5c8d7c4e206be9efb1b22a463441dd22", + "Clone1_N3.trim_fastqc.zip:md5,e255d55c6693f6891484c97c2b3a64b0" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:15:01.578725616" + }, + "untar": { + "content": [ + "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", + "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", + "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", + "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", + "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", + "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:14:50.348773909" + }, + "multiqc": { + "content": [ + "fastqc-status-check-heatmap.txt:md5,30f55902420433a11971d36956e8576e", + "fastp_filtered_reads_plot.txt:md5,0af4d3cfbf463f33b2b88cdfd69909ac", + "fastqc_overrepresented_sequences_plot.txt:md5,d861a4a956a3023efa19b1259d8665b2", + "fastqc_top_overrepresented_sequences_table-1.txt:md5,928ade897074cb3ad411bcd31f504dd2", + "fastqc_sequence_counts_plot-1.txt:md5,37d8ae6c5734eb2679e65e46c9af9101", + "mirtrace_complexity_plot.txt:md5,5f78d6f559a9642e68e1fd74ac2c11ca", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", + "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", + "samtools-stats-dp.txt:md5,0f88cdcc523ea239c2dd7e1e2decec36", + "fastqc_sequence_length_distribution_plot.txt:md5,13f72b3be854c74cd7b5176ca0583770", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "fastqc_sequence_duplication_levels_plot-1.txt:md5,06a4162d4787883b1f39a1b9acb7bb91", + "fastqc_per_base_sequence_quality_plot-1.txt:md5,6a0df664a369ee216412f0033ed3a042", + "multiqc_general_stats.txt:md5,5097cefe7b3b0d0503eacf9e81e9b51e", + "fastqc_per_base_n_content_plot-1.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "fastqc_per_base_n_content_plot.txt:md5,fb8a49467d1679dbf716e1f00c1f25e5", + "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,b1481a9fbf5ea541b39aed99b51d616f", + "fastqc_per_sequence_quality_scores_plot.txt:md5,38dbd6509de7f1beac17e44acb8336be", + "mirtrace_qc_plot.txt:md5,c436d017382baed6617fc3c1ad8ab41d", + "fastqc_per_sequence_quality_scores_plot-1.txt:md5,69f4459318311103fe71a5d1d3b2c076", + "mirtrace_length_plot.txt:md5,2366f10eb8bd3c32d2b35e2df20c786c", + "fastqc_top_overrepresented_sequences_table.txt:md5,9acec391e0a46858e110f5baa65fb0a9", + "fastqc_overrepresented_sequences_plot-1.txt:md5,1de000de50cc7516bb9d996def14c6eb", + "fastqc-status-check-heatmap-1.txt:md5,e64c353797e6dc057d10b3194ca6b20d", + "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", + "mirtrace_rna_categories_plot.txt:md5,8665376e2a123e1661f82cbbee54789f", + "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", + "samtools_alignment_plot.txt:md5,ac24d7f3bf5858e7550d2f93446137e1", + "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", + "mirtop_read_count_plot.txt:md5,29cce56b45edc10ff63badfa49eaf6b9", + "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "mirtop_unique_read_count_plot.txt:md5,b540743844ef0cdb81390b9db1d23afe", + "mirtop_mean_read_count_plot.txt:md5,837e240c5ecd10b95257e65fcd9f8393", + "fastqc_adapter_content_plot.txt:md5,86a0f478fd3e690ef5132d08bf4e7625", + "fastqc_sequence_duplication_levels_plot.txt:md5,88b0babe77f623547e8af664791ef2d0", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,539883757ae5bf731da93fe0568022e9", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,ed7205b9c46d5f431c5b3bf499a673a1", + "fastqc_adapter_content_plot-1.txt:md5,71ba0983a71f3a833526ab83a985d072", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,a8387a3e6b350acd16bb0ed5a43949d8", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3e9c1a7204c12d9c1b3b53342cf61840", + "multiqc_sources.txt:md5,d5202aca3585fa8914aa600bea4825e1", + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,efa8123c9ad43f99a6fba671f50322ca" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:14:50.192712649" + }, + "mirna_quant": { + "content": [ + "Control_N1_mature_hairpin.sorted.stats:md5,feb69ad2f8bbc527e39502a297f08abd", + "Control_N1_mature_hairpin.sorted.idxstats:md5,e1f455195f1cb42a1d1e58770aaeb2b4", + "Clone1_N3_mature_hairpin.sorted.flagstat:md5,6f14ec4cd502c0eb213b1905b4568a76", + "Clone9_N2_mature_hairpin.sorted.stats:md5,7bb8654d44dac245aec6aa045250628a", + "Clone9_N3_mature_hairpin.sorted.flagstat:md5,efc65cb620ca139b19967e12f13ba007", + "Control_N1_mature_hairpin.sorted.bam.bai:md5,28b1225b55f40c3537de733de9a6768f", + "Control_N3_mature_hairpin.sorted.bam.bai:md5,c15c68783029019acf79b392384cf0b4", + "Control_N1_mature_hairpin.sorted.flagstat:md5,41769a400a176ea78432749f07f80fda", + "Control_N1_mature_hairpin.sorted.bam:md5,ff9eaccd9de8616315ac1cc19d01547a", + "Clone9_N1_mature_hairpin.sorted.stats:md5,155f327a9be0afa9584ec426826b5457", + "Clone1_N3_mature_hairpin.sorted.bam:md5,0468b44c0c5fa22a027cfc9abe8f0386", + "Control_N2_mature_hairpin.sorted.stats:md5,1195dd51f77e338db83dc66476ac7c5f", + "Clone9_N1_mature_hairpin.sorted.bam.bai:md5,b545947ebeb48b941a0ff77c463da13d", + "Control_N3_mature_hairpin.sorted.idxstats:md5,2c44710ce63bdebb12d64c729ef338b0", + "Control_N2_mature_hairpin.sorted.bam.bai:md5,fc6c5ea2d38928afad19a85ea7b51b47", + "Clone1_N3_mature_hairpin.sorted.bam.bai:md5,302937440b1786922a8f2d1659ba6a6e", + "Clone1_N1_mature_hairpin.sorted.idxstats:md5,0bca2d01f734128f3c11cf2697433048", + "Clone9_N3_mature_hairpin.sorted.idxstats:md5,9523d29d411c2efb0a1756355230fa98", + "Control_N2_mature_hairpin.sorted.idxstats:md5,8859b6e432cef8b24d5fb258a06aaabe", + "Clone9_N2_mature_hairpin.sorted.flagstat:md5,663ae0bb8b29d1e1c3d75ef5df1015a4", + "Clone9_N1_mature_hairpin.sorted.flagstat:md5,3e4b295b54df05c438603edaa53123b1", + "Control_N3_mature_hairpin.sorted.flagstat:md5,f3df866b94dc6ef355b01f22047aaf4f", + "Clone1_N1_mature_hairpin.sorted.bam.bai:md5,914846c8ffea1fa43a4799b8cc90ac1e", + "Clone1_N1_mature_hairpin.sorted.bam:md5,6a2302ef9acb50511e0894d7d94a7d38", + "Control_N3_mature_hairpin.sorted.bam:md5,8cf19f32d26228983c961c0d978358db", + "Clone9_N3_mature_hairpin.sorted.stats:md5,9f61c028bb1c92667e31093156ada662", + "Clone1_N1_mature_hairpin.sorted.stats:md5,bd02cb15e666054edecc89d392d72902", + "Clone9_N2_mature_hairpin.sorted.idxstats:md5,04b1c0ea4f133b5ee9086eec1f4077e7", + "Clone1_N3_mature_hairpin.sorted.stats:md5,471db325d8ccd1fe787b5dd91dccf487", + "Clone9_N3_mature_hairpin.sorted.bam.bai:md5,3b745be9c28f88bcacbf1da3eafd63ad", + "Control_N2_mature_hairpin.sorted.flagstat:md5,2605548b5ab1e6ad6b5cf88ea0030909", + "Clone9_N1_mature_hairpin.sorted.idxstats:md5,238b462a2418d545418c0b3a28029bdf", + "Clone9_N2_mature_hairpin.sorted.bam.bai:md5,420327a97d9178d89170a5611a02d827", + "Control_N3_mature_hairpin.sorted.stats:md5,2f2249c537451d1f72dfe298f16093ac", + "Clone9_N1_mature_hairpin.sorted.bam:md5,71333f26f0ac943ced66c9358e804158", + "Clone9_N2_mature_hairpin.sorted.bam:md5,53e1e9289d60fdd1d3b9820af5064dd3", + "Clone1_N1_mature_hairpin.sorted.flagstat:md5,8d0c785fec7b300200863c68b158444c", + "Control_N2_mature_hairpin.sorted.bam:md5,79a584d7c68f57697257cda41e6b6ccf", + "Clone9_N3_mature_hairpin.sorted.bam:md5,946f27f50f1658c64c2c222c2f37d2b8", + "Clone1_N3_mature_hairpin.sorted.idxstats:md5,5b6cd8d5784c387d2649f18499a17c6e", + "Control_N1_mature.sorted.bam.bai:md5,9ad0d0c840f6335ae7227cfdf03f714a", + "Clone1_N1_mature.sorted.stats:md5,9c42ffda181ca24ab076efc16fcfd4b3", + "Clone1_N3_mature.sorted.idxstats:md5,805f115ac4d9c8033908bafaba6c92fb", + "Clone9_N2_mature.sorted.stats:md5,fb8c403012481dafb895013c555f6d85", + "Control_N2_mature.sorted.stats:md5,ef5935898e3ca45d898053af335d1dfb", + "Control_N3_mature.sorted.flagstat:md5,2831f55bccbcf666d1c313ef377bcb30", + "Clone9_N3_mature.sorted.bam:md5,6a20122570543da6042a94fade945407", + "Clone9_N1_mature.sorted.bam.bai:md5,0d1a7dbe6e97f7fa4811790e6640c978", + "Clone9_N3_mature.sorted.stats:md5,23b012dd60ea6dcec5cedb5a73ffc792", + "Clone1_N1_mature.sorted.bam:md5,dc305cfe5c54b93e5b91b00dba676780", + "Clone1_N3_mature.sorted.flagstat:md5,67fc6ba8516d4e5b3ed2a62febc92f0a", + "Clone9_N1_mature.sorted.idxstats:md5,c6eb22f3ff675e422d065375279150b2", + "Control_N1_mature.sorted.bam:md5,1c6e2e02df78ae15c535726b448e3704", + "Control_N1_mature.sorted.stats:md5,b4ffb3a7623e32420def4d3470a326ab", + "Control_N1_mature.sorted.idxstats:md5,847bc5c6ef44e1f9754e47e648a5ef98", + "Clone9_N2_mature.sorted.flagstat:md5,247e02da50509fc1b3c5b35001922a8d", + "Control_N2_mature.sorted.flagstat:md5,c8742d1b49535ff815c2def66cba681e", + "Control_N2_mature.sorted.bam.bai:md5,01e9905b9d121d3c0341488bade69180", + "Control_N2_mature.sorted.bam:md5,57f6e91f83799f8b9cbc739a1a28ab78", + "Clone9_N2_mature.sorted.bam.bai:md5,a68809526ec55ae96f6eb62a170ac5ca", + "Control_N2_mature.sorted.idxstats:md5,12388de965d69b6102b62bc9cdf27e85", + "Control_N3_mature.sorted.bam.bai:md5,720f79c56ab38ba1ebafeb9c0fe5cf45", + "Clone9_N1_mature.sorted.flagstat:md5,014b846757652783ff3f954a966b8a1b", + "Clone9_N2_mature.sorted.bam:md5,d96c5b1d9f1111936037a605043becdf", + "Clone1_N3_mature.sorted.bam.bai:md5,567e08c765069502219a2bf080a84600", + "Clone9_N3_mature.sorted.idxstats:md5,dee54e8e22dfca24acc290bf89a05cd4", + "Clone9_N2_mature.sorted.idxstats:md5,c9643d610de2f4d449a876e41dcab872", + "Clone9_N3_mature.sorted.flagstat:md5,4f60cfd3527e91df204253f9f1aebfcd", + "Control_N3_mature.sorted.idxstats:md5,5fb7b46915043bd3c947a37afc3e8075", + "Clone9_N3_mature.sorted.bam.bai:md5,b1ac22e2ceb13f78bcede9cef82d2989", + "Clone1_N1_mature.sorted.bam.bai:md5,6b5783e42dca72415ed9cc25cd94b6cb", + "Clone1_N1_mature.sorted.idxstats:md5,77ed64ddd23cf07340b65c04559d4726", + "Control_N3_mature.sorted.bam:md5,19a7b1b8801094562492576c28ec33c7", + "Clone1_N1_mature.sorted.flagstat:md5,f138a532bc7dab94f7cf4b4a4e5e23e5", + "Control_N3_mature.sorted.stats:md5,ff9dab4d3220aa44cdc80ea2fc311823", + "Clone1_N3_mature.sorted.stats:md5,e8feced949af44c8e5d31523b12122b9", + "Clone1_N3_mature.sorted.bam:md5,6176d098a0384709aa5d3589258c701d", + "Clone9_N1_mature.sorted.bam:md5,7a1024fc323335f31ebc8297dd789fc2", + "Control_N1_mature.sorted.flagstat:md5,16318a574fe410b81c0e2cdf0dfa3c97", + "Clone9_N1_mature.sorted.stats:md5,02184884c17c8730f4df9e1a6144bbdc", + "mirna.tsv:md5,1f840afe7ab68eac73feaaad321b64f6", + "mirtop.tsv:md5,8401bbe98e85a6d8b1ab7466d2e178ac", + "mirtop.gff:md5,57cc78c6e20626b41ec833dda81c40d1", + "mirtop_rawData.tsv:md5,774410dd2cf1e5be83bf8d6e1e8b96b0", + "mirtop_stats.txt:md5,8b1ce9988d872c72ab3b23ed43000f7c", + "Clone1_N3.fastp_trimmed.fastq.gz:md5,2e395240c74b3870efe03dc329d8bad8", + "Control_N1.fastp_trimmed.fastq.gz:md5,2f09082eb68a8f1dc308050e330887ec", + "Control_N3.fastp_trimmed.fastq.gz:md5,342368a6e6acdaf0ae9379676b6d07f0", + "Clone9_N1.fastp_trimmed.fastq.gz:md5,115cf0c346a93a47ba782c5724b4f090", + "Clone1_N1.fastp_trimmed.fastq.gz:md5,14a2590e663dbde105780726c2173c25", + "Clone9_N2.fastp_trimmed.fastq.gz:md5,c922ec95a4b84d806dd2054ff0f9cab7", + "Clone9_N3.fastp_trimmed.fastq.gz:md5,67cf9a7d2fa431f0e772391ed1651f93", + "Control_N2.fastp_trimmed.fastq.gz:md5,d6e607edcb3d71c546ce8fdfb18e3999", + "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", + "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", + "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "mature_unmapped_read_counts.txt:md5,41348458c2a8874dcb8a82a30c3f0e43", + "mature_normalized_CPM.txt:md5,88c481df2e8b073ebfaf440620a2cd2a", + "hairpin_logtpm.csv:md5,87f2d92a9ca3ed5390b4cc903776fde4", + "mature_logtpm.txt:md5,c5cd8a9a2176af9d0f7759f92233929d", + "mature_edgeR_MDS_plot_coordinates.txt:md5,29584c2e2e2378a91e891a628f63a892", + "hairpin_unmapped_read_counts.txt:md5,7618d6bdc018e5712343bf4eb8d94fa4", + "mature_edgeR_MDS_distance_matrix.txt:md5,974273c499e26854e27c2cdbe9fa5f2c", + "mature_log2CPM_sample_distances.txt:md5,bea4b11907cd6badbc68e9b505a48bb8", + "hairpin_log2CPM_sample_distances.txt:md5,b19fa1d9f821fc8e2c0e9f34f76b5479", + "hairpin_edgeR_MDS_distance_matrix.txt:md5,c8377298e59143e17f9d0822c83059c3", + "hairpin_logtpm.txt:md5,96d146b5de6066b609b56a2344dfde67", + "hairpin_edgeR_MDS_plot_coordinates.txt:md5,dedaa69ffc330ce3b61593f2c58054e3", + "mature_logtpm.csv:md5,1a22f980708232227336118a8212fa32", + "hairpin_normalized_CPM.txt:md5,02e3803d5a9b0e2f4be94fac0cb94429", + "mature_counts.csv:md5,4d9f320ae04949cc0111bd90e2a2587d", + "hairpin_counts.csv:md5,fd30079c785a28327226d7c51b68b9cc" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:14:50.931370818" + } +} \ No newline at end of file diff --git a/tests/test_no_genome.nf.test b/tests/test_no_genome.nf.test index 3fbb6cd7..3b502706 100644 --- a/tests/test_no_genome.nf.test +++ b/tests/test_no_genome.nf.test @@ -10,7 +10,7 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } } @@ -19,203 +19,258 @@ nextflow_pipeline { { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, { assert workflow.trace.succeeded().size() == 147 }, + { assert snapshot( - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/Control_N2_seqcluster.bam"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") + ).match("bowtie_index") }, + + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), + path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") + ).match("multiqc") }, + + { assert snapshot( + path("$outputDir/mirna_quant/bam/seqcluster/Control_N3_seqcluster.bam"), path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N3_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N1_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N3_seqcluster.bam"), + path("$outputDir/mirna_quant/bam/seqcluster/Control_N1_seqcluster.bam"), path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N2_seqcluster.bam"), + path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N3_seqcluster.bam"), path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N1_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Control_N1_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Control_N3_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N2_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N3_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N1_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N3_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/Control_N2_seqcluster.bam"), + path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N1_seqcluster.bam"), path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N2_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N1_seqcluster_unmapped.fq.gz"), path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N1_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N3_seqcluster_unmapped.fq.gz"), path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N1_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N3_seqcluster_unmapped.fq.gz"), path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N3_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N2_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N1_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N1_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N3_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N2_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N2_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N3_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N3_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N1_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.bam"), path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.bam"), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N2_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N3_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone1_N3_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N3_mature_unmapped.fq.gz"), path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N1_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N2_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N3_mature_unmapped.fq.gz"), path("$outputDir/mirna_quant/bam/mature/unmapped/Clone1_N1_mature_unmapped.fq.gz"), path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N1_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N3_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N2_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N3_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N3_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N2_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N1_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N1_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N1_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N3_mature_hairpin_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N2_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone1_N3_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N2_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), path("$outputDir/mirna_quant/mirtop/mirtop.gff"), path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt") + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") ).match("mirna_quant") }, + { assert snapshot( - path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip"), path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip"), path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip"), + path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip"), path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip"), path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip"), path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip"), path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip") + path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip") ).match("fastqc") }, + { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), @@ -223,37 +278,17 @@ nextflow_pipeline { path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta") + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") ).match("mirtrace") }, - { assert snapshot( - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt") - ).match("bowtie_index") }, - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/multiqc_fastqc.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_contamination.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_length.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_software_versions.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtop.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_complexity.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_samtools_stats.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_fastqc_1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_fastp.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_mirtrace_summary.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt") - ).match("multiqc") }, + ) } diff --git a/tests/test_no_genome.nf.test.snap b/tests/test_no_genome.nf.test.snap new file mode 100644 index 00000000..2e8a572d --- /dev/null +++ b/tests/test_no_genome.nf.test.snap @@ -0,0 +1,311 @@ +{ + "bowtie_index": { + "content": [ + "fasta_bidx.3.ebwt:md5,cccaad86d0d5e5f3c1d4ca3a700ee980", + "fasta_bidx.1.ebwt:md5,9935201150ff358248380e07219fe093", + "fasta_bidx.rev.1.ebwt:md5,5e75ec9fb284ba316b3982a93f4ded49", + "fasta_bidx.rev.2.ebwt:md5,ba8e745f11b3d28240a78efd5bf2a7b0", + "fasta_bidx.4.ebwt:md5,96e2e8ec9f02d324d845e0708ff4b552", + "fasta_bidx.2.ebwt:md5,9cf18dd788535404d7fd6a62450d2ce0", + "fasta_bidx.3.ebwt:md5,a6d3abdddbf80cb9b2c97bbd7bc1f084", + "fasta_bidx.1.ebwt:md5,a2162fb747e95535ea5a67023b8961cf", + "fasta_bidx.rev.1.ebwt:md5,27578696198a61b0a3f783802823337e", + "fasta_bidx.rev.2.ebwt:md5,726c60d9a0108739ba9b61774bc39633", + "fasta_bidx.4.ebwt:md5,62e35549f28a1a85ccaf35858b1726aa", + "fasta_bidx.2.ebwt:md5,876ebed9375cda6f248dfc940308fa5e" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:24:10.78656165" + }, + "mirtrace": { + "content": [ + "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", + 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"Clone9_N1_mature_hairpin.sorted.idxstats:md5,2c376fd533eaa5bfd321657e8cdfc9f1", + "Clone9_N2_mature_hairpin.sorted.bam.bai:md5,22cb9d52da218bae97710d42ff3142e1", + "Control_N3_mature_hairpin.sorted.stats:md5,55cac79ae09a6147ffba190d6115bfa4", + "Clone9_N1_mature_hairpin.sorted.bam:md5,f8be17f518dc9b7af0c5c33fbc543b3e", + "Clone9_N2_mature_hairpin.sorted.bam:md5,c34bc408ec180d49ebadfbcfabbf07a6", + "Clone1_N1_mature_hairpin.sorted.flagstat:md5,b2e8eb3b3d10a01a3794e2410c3ba270", + "Control_N2_mature_hairpin.sorted.bam:md5,ddc5d52a3cce2eac8a0157ad35df4f8b", + "Clone1_N1_mature_hairpin.bam:md5,99e73f811e024126e48e60dd50c44ae7", + "Clone9_N3_mature_hairpin.sorted.bam:md5,36132af606f4dd66a69a93ca20dd2fc8", + "Clone1_N3_mature_hairpin.sorted.idxstats:md5,a2457f5571563ecc03c4d9834fa75da0", + "Clone9_N1_mature_hairpin_unmapped.fq.gz:md5,2f0664e028c76f624d95af52df5b9988", + "Clone1_N1_mature_hairpin_unmapped.fq.gz:md5,77a17714c20e52c8f7a3a4a5b85c2cb3", + "Clone1_N3_mature_hairpin_unmapped.fq.gz:md5,901909393df6f5a36e13544f3e856aff", + "Clone9_N2_mature_hairpin_unmapped.fq.gz:md5,842987019b7ee22e0b3c3e454dad090f", + "Control_N2_mature_hairpin_unmapped.fq.gz:md5,984f690e586f2066fd3959bb26e1b2a9", + "Control_N3_mature_hairpin_unmapped.fq.gz:md5,50f499525a898e9145f9aad2d70bbed7", + "Clone9_N3_mature_hairpin_unmapped.fq.gz:md5,ea15bcefa3a9a69d4c22bb555f672851", + "Control_N1_mature_hairpin_unmapped.fq.gz:md5,2a0cda6eb6fb2cd06304fd69a4483dec", + "Control_N3_mature.bam:md5,75ca5d98d0aaaa9d693c56d90de1a045", + "Control_N1_mature.sorted.bam.bai:md5,187f273f39c4459cc6dae5dbe6943a84", + "Clone1_N1_mature.sorted.stats:md5,9c42ffda181ca24ab076efc16fcfd4b3", + "Clone1_N3_mature.sorted.idxstats:md5,39e30f2f398992208a5411c74a3c9774", + "Clone9_N2_mature.sorted.stats:md5,fb8c403012481dafb895013c555f6d85", + "Control_N2_mature.sorted.stats:md5,958b7a9ccfe3893b117317d00cd29949", + "Control_N3_mature.sorted.flagstat:md5,2831f55bccbcf666d1c313ef377bcb30", + "Clone9_N3_mature.sorted.bam:md5,1a1d3c718b2d61ff0df5af08b3a270b8", + "Clone9_N1_mature.sorted.bam.bai:md5,792064a331dcee563f2c9d89131257fc", + "Control_N2_mature.bam:md5,6b8bbe7b346e16738fb3054d7aff1d6d", + "Clone9_N3_mature.sorted.stats:md5,23b012dd60ea6dcec5cedb5a73ffc792", + "Clone1_N1_mature.sorted.bam:md5,94f2c8de0d832e161603ac13c04a80dc", + "Clone1_N3_mature.sorted.flagstat:md5,67fc6ba8516d4e5b3ed2a62febc92f0a", + "Clone9_N1_mature.sorted.idxstats:md5,4f5c53b3acc6ee228d5f5766bb4bf1d4", + "Control_N1_mature.sorted.bam:md5,b1f791c7c05ed79a7e0dcecd621ffb98", + "Control_N1_mature.sorted.stats:md5,b4ffb3a7623e32420def4d3470a326ab", + "Control_N1_mature.sorted.idxstats:md5,ec6150327db493da8faaca1525afacd1", + "Clone9_N2_mature.sorted.flagstat:md5,247e02da50509fc1b3c5b35001922a8d", + "Control_N2_mature.sorted.flagstat:md5,cdeb62c8bd17760b6d258a17bec1e80c", + "Clone1_N1_mature.bam:md5,a4bdd9fe63b0c46558785803c8a2c38a", + "Control_N2_mature.sorted.bam.bai:md5,6099ef1e91998df723db75f4f310a0a7", + "Control_N2_mature.sorted.bam:md5,77ca8d740b118d54396d811aea35aa25", + "Clone9_N2_mature.sorted.bam.bai:md5,dccf48ac51c38a86e54e7a7e8de442ab", + "Control_N2_mature.sorted.idxstats:md5,af6ecc38643b1aedf67354e91e95364e", + "Control_N3_mature.sorted.bam.bai:md5,ec26ee658ce263355991aa9b270fe8bb", + "Clone9_N1_mature.sorted.flagstat:md5,014b846757652783ff3f954a966b8a1b", + "Clone9_N2_mature.sorted.bam:md5,b3fd17a677e4b542217d011c54a3b825", + "Clone1_N3_mature.sorted.bam.bai:md5,4a9bef5bdb5e80d47f5d67a8860e3160", + "Clone9_N3_mature.sorted.idxstats:md5,84784ae05dce03ca691f7ae0b4074eb3", + "Clone1_N3_mature.bam:md5,e5898ea3b269fec3e0bd84671a8bcd8d", + "Clone9_N2_mature.sorted.idxstats:md5,1ecdffcf833b08768c83bd74bf5e1a95", + "Clone9_N3_mature.bam:md5,7246c160a0e78d0d0ee06ebfbda26877", + "Clone9_N3_mature.sorted.flagstat:md5,4f60cfd3527e91df204253f9f1aebfcd", + "Control_N3_mature.sorted.idxstats:md5,a38cb5edff03d442729ad3ab2dad5425", + "Control_N1_mature.bam:md5,9704faaff4a86e380e0c882099c73dc1", + "Clone9_N3_mature.sorted.bam.bai:md5,1e1d39c7abe355e3cecbbb4fc2173d94", + "Clone1_N1_mature.sorted.bam.bai:md5,5c3f93a439aee824b63756b6d3281acb", + "Clone1_N1_mature.sorted.idxstats:md5,69adbd609e315faaa5b03082919c941f", + "Control_N3_mature.sorted.bam:md5,f76a7e2f9c398ed662f9c1e58d095025", + "Clone1_N1_mature.sorted.flagstat:md5,f138a532bc7dab94f7cf4b4a4e5e23e5", + "Control_N3_mature.sorted.stats:md5,ff9dab4d3220aa44cdc80ea2fc311823", + "Clone9_N2_mature.bam:md5,6c35427293dd2ece2c95b81dad913ad8", + "Clone1_N3_mature.sorted.stats:md5,e8feced949af44c8e5d31523b12122b9", + "Clone1_N3_mature.sorted.bam:md5,a760ed85ecc686e3f84f7ff16ed924ef", + "Clone9_N1_mature.sorted.bam:md5,8af13c91caa7493b4f07d2d412f5548c", + "Clone9_N1_mature.bam:md5,f5e4c52412c28c222113010879993235", + "Control_N1_mature.sorted.flagstat:md5,16318a574fe410b81c0e2cdf0dfa3c97", + "Clone9_N1_mature.sorted.stats:md5,02184884c17c8730f4df9e1a6144bbdc", + "Control_N3_mature_unmapped.fq.gz:md5,7342270d6c56f5963975616dfbd1ea7b", + "Control_N1_mature_unmapped.fq.gz:md5,d3619daf05993c74778b56124a1c9b0b", + "Clone9_N3_mature_unmapped.fq.gz:md5,96963c170975470e839ee12287406b6f", + "Clone1_N1_mature_unmapped.fq.gz:md5,ba4ccae731a04630b51e2357f8eee62a", + "Clone9_N1_mature_unmapped.fq.gz:md5,d59e0d22095886c30c79a7e440d2181f", + "Clone9_N2_mature_unmapped.fq.gz:md5,a0bd26697f8745406bfe97b5c34985e8", + "Clone1_N3_mature_unmapped.fq.gz:md5,4b2e947182f383eed7a742fbb0cb7fb4", + "Control_N2_mature_unmapped.fq.gz:md5,4d6e259f01d963365ed90862c16ab473", + "mirna.tsv:md5,01179dda321cf235df8c1fb72609ecb4", + "mirtop.tsv:md5,544a9859d5cfb8083fdea86f36ecd7af", + "mirtop.gff:md5,f6220d75e81e67be3fbbd0251ce2947b", + "mirtop_rawData.tsv:md5,98c46ade3ba0b141f1306c1dbc9a3ff1", + "mirtop_stats.txt:md5,b28c2f920f1e73f827f32fdd31654cbd", + "Clone1_N3.fastp_trimmed.fastq.gz:md5,2e395240c74b3870efe03dc329d8bad8", + "Control_N1.fastp_trimmed.fastq.gz:md5,2f09082eb68a8f1dc308050e330887ec", + "Control_N3.fastp_trimmed.fastq.gz:md5,342368a6e6acdaf0ae9379676b6d07f0", + "Clone9_N1.fastp_trimmed.fastq.gz:md5,115cf0c346a93a47ba782c5724b4f090", + "Clone1_N1.fastp_trimmed.fastq.gz:md5,14a2590e663dbde105780726c2173c25", + "Clone9_N2.fastp_trimmed.fastq.gz:md5,c922ec95a4b84d806dd2054ff0f9cab7", + "Clone9_N3.fastp_trimmed.fastq.gz:md5,67cf9a7d2fa431f0e772391ed1651f93", + "Control_N2.fastp_trimmed.fastq.gz:md5,d6e607edcb3d71c546ce8fdfb18e3999", + "hairpin.fa_igenome.fa_idx.fa:md5,f7ee61ca4537300386fdb85c7dec24d2", + "mature.fa_igenome.fa_idx.fa:md5,48215f56ca0bfbdbb1a28482457283e3", + "hairpin.fa_igenome.fa:md5,cddcc379892cb43e807ff54feafafbc1", + "mature.fa_igenome.fa:md5,48215f56ca0bfbdbb1a28482457283e3", + "mature_unmapped_read_counts.txt:md5,edc81b30c58368abb964fe13310f9c04", + "mature_normalized_CPM.txt:md5,d8d8712785f930456e8e739c4081ccbb", + "hairpin_logtpm.csv:md5,2d1c128288f7d8aa8ea870d488fb0586", + "mature_logtpm.txt:md5,b47a967bbd764361beffe188ae31d278", + "mature_edgeR_MDS_plot_coordinates.txt:md5,af754c03339430a71c0998d8f0580e68", + "hairpin_unmapped_read_counts.txt:md5,b81d5b91da9af7eb747ab8b6a9243e26", + "mature_edgeR_MDS_distance_matrix.txt:md5,18533a2afb0a6fad6be1d879690111f7", + "mature_log2CPM_sample_distances.txt:md5,980bba51cd88ae0c8ac418fe653492af", + "hairpin_log2CPM_sample_distances.txt:md5,7cca5268281ff6e24f849526589b9e48", + "hairpin_edgeR_MDS_distance_matrix.txt:md5,fcd5a68b940856b28eac2ea029f61967", + "hairpin_logtpm.txt:md5,912a1604f482d5b4bb54199b0f07c6eb", + "hairpin_edgeR_MDS_plot_coordinates.txt:md5,cbef839bb66d6e832243df2bd46d4ebd", + "mature_logtpm.csv:md5,120c6af7180855ba68098685ca81c392", + "hairpin_normalized_CPM.txt:md5,47a03cbecaf025fdcebdb17148ace558", + "mature_counts.csv:md5,2ffb977afc7b61a79056c2868cd53222", + "hairpin_counts.csv:md5,118236c7fa7b56fa78e495582eaf285d" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:24:11.083677532" + } +} \ No newline at end of file diff --git a/tests/test_technical_repeats.nf.test b/tests/test_technical_repeats.nf.test index 4d7659e2..22f5accf 100644 --- a/tests/test_technical_repeats.nf.test +++ b/tests/test_technical_repeats.nf.test @@ -10,7 +10,7 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } } @@ -19,94 +19,115 @@ nextflow_pipeline { { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, { assert workflow.trace.succeeded().size() == 75 }, + { assert snapshot( - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), + path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.edited.fa"), + path("$outputDir/bowtie_index/genome/genome.3.ebwt"), + path("$outputDir/bowtie_index/genome/genome.4.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") + ).match("bowtie_index") }, + + { assert snapshot( + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai") + ).match("genome_quant") }, + + { assert snapshot( + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), path("$outputDir/mirna_quant/mirtop/mirtop.gff"), path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt") + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") ).match("mirna_quant") }, + { assert snapshot( - path("$outputDir/bowtie_index/genome/genome.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.4.ebwt"), - path("$outputDir/bowtie_index/genome/genome.3.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.edited.fa"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt") - ).match("bowtie_index") }, - { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), @@ -115,23 +136,7 @@ nextflow_pipeline { path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") ).match("mirtrace") }, - { assert snapshot( - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats") - ).match("genome_quant") }, + ) } diff --git a/tests/test_technical_repeats.nf.test.snap b/tests/test_technical_repeats.nf.test.snap new file mode 100644 index 00000000..f18a5b4c --- /dev/null +++ b/tests/test_technical_repeats.nf.test.snap @@ -0,0 +1,153 @@ +{ + "bowtie_index": { + "content": [ + "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", + "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", + "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", + "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", + "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", + "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", + "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", + "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", + "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", + "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", + "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", + "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", + "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", + "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", + "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", + "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", + "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", + "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", + "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:39:09.347754579" + }, + "mirtrace": { + "content": [ + "mirtrace-stats-rnatype.tsv:md5,2843855add34a73acd332a112bd80a34", + "mirtrace-stats-length.tsv:md5,71591c754eed9db419b91fb499f8e2ab", + "mirtrace-stats-contamination_detailed.tsv:md5,c16e27cc433dacdd5bfff09a9aaab736", + "mirtrace-stats-qcstatus.tsv:md5,37465e5d4d756792b95f187e6406fc6b", + "mirtrace-stats-contamination_basic.tsv:md5,ca3f99b1b89d2674864b62bbf9c41592", + "mirtrace-stats-phred.tsv:md5,1ac6fdae848cc4e39904edc361f75d1f", + "mirtrace-stats-mirna-complexity.tsv:md5,c69c4762a887a8e792c896dc5d3866b8", + "Clone1_N1.fastp.fasta:md5,7630d5d8f047d2f7e9492598e6f97c84", + "Control_N1.fastp.fasta:md5,534de89c8354a874458497804dcb7785", + "Clone9_N3.fastp.fasta:md5,0f2ef6c209a0b591d4eff5d77b713957", + "Clone1_N1.fastp.fasta:md5,f49d63f3d05aeb349f58f2bb95552332", + "Control_N1.fastp.fasta:md5,b34c20e0736351db5d0d1d3236de18ec", + "Clone9_N3.fastp.fasta:md5,726d1d14a88d7b816bb97bab9f006c45" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:39:17.175802364" + }, + "genome_quant": { + "content": [ + "Control_N1_mature_hairpin_genome.sorted.flagstat:md5,41e0b4dc62f9b8779534d67630ea6ab6", + "Clone9_N3_mature_hairpin_genome.sorted.stats:md5,872a90aca4d070f9403ae86b42666e2c", + "Clone9_N3_mature_hairpin_genome.sorted.flagstat:md5,50eb08817350b22dbe99bcc3dc7f2a38", + "Clone1_N1_mature_hairpin_genome.sorted.flagstat:md5,1d56901f0754350ee0925cff76bee6d1", + "Clone1_N1_mature_hairpin_genome.sorted.bam:md5,aee26f20d3188c9e0c17c8b19ee01068", + "Clone1_N1_mature_hairpin_genome.sorted.bam.bai:md5,bf5167b68a29df979ea14a3cb148c4ac", + "Clone9_N3_mature_hairpin_genome.sorted.bam:md5,b80e7a38ab0f940047d39cd8ef3e1905", + "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,964b1ec118f45c5cb9443efc996b4b3e", + "Control_N1_mature_hairpin_genome.sorted.bam:md5,d153cfca67b7fd8fee388b22302c20c7", + "Control_N1_mature_hairpin_genome.sorted.idxstats:md5,6f43b2104f522103671ce78dc7d75b6d", + "Control_N1_mature_hairpin_genome.sorted.stats:md5,97f2c3ceb62b98d9169b226e954a1150", + "Control_N1_mature_hairpin_genome.sorted.bam.bai:md5,dc7706620275f5a43b52066970c1474d", + "Clone9_N3_mature_hairpin_genome.sorted.idxstats:md5,6561bdbc8589548d965823d7f43dee39", + "Clone1_N1_mature_hairpin_genome.sorted.idxstats:md5,f6408e25770f9a8530126900c314332f", + "Clone9_N3_mature_hairpin_genome.sorted.bam.bai:md5,5fa626110a289ede3549c4c73b53d714" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:39:09.615825899" + }, + "software_versions": { + "content": [ + "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, CAT_FASTQ={cat=8.3}, FASTP={fastp=0.23.4}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_GENOME={bowtie=1.3.1}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:39:09.345801293" + }, + "mirna_quant": { + "content": [ + "Control_N1_mature_hairpin.sorted.stats:md5,41ed031d9ee3d775fab782beea7c2c5e", + "Control_N1_mature_hairpin.sorted.idxstats:md5,2bb41d5a20116c7457ef45c1b294d22d", + "Clone9_N3_mature_hairpin.sorted.flagstat:md5,79f3d50c45d9aa0d2525f5f1411e8dd5", + "Control_N1_mature_hairpin.sorted.bam.bai:md5,b901e66cbdd91b38b32c49671c2b0538", + "Control_N1_mature_hairpin.sorted.flagstat:md5,e727c4751070cf76ebfd484c0e37d990", + "Control_N1_mature_hairpin.sorted.bam:md5,579a1e43d1a6205ac2c118c1b39bbdae", + "Clone1_N1_mature_hairpin.sorted.idxstats:md5,f2a16cf301d8cfd5f9f99edb610705c7", + "Clone9_N3_mature_hairpin.sorted.idxstats:md5,98db6ef38c05a65ee7ef5a7520f4f51c", + "Clone1_N1_mature_hairpin.sorted.bam.bai:md5,4bd9a2f4353cdc65a1db6edbdbab7a82", + "Clone1_N1_mature_hairpin.sorted.bam:md5,9557cc47f4e70261cc583b81fd3c55dd", + "Clone9_N3_mature_hairpin.sorted.stats:md5,52d607b29c6fae0a72cb55b83a5d550f", + "Clone1_N1_mature_hairpin.sorted.stats:md5,3fc6353abadc1c6e2687bc7a081f93a2", + "Clone9_N3_mature_hairpin.sorted.bam.bai:md5,75f78a876d94179713ce913a1dc43a79", + "Clone1_N1_mature_hairpin.sorted.flagstat:md5,f6d7848cf9c70cd3469ce1944d17be3c", + "Clone9_N3_mature_hairpin.sorted.bam:md5,d04faf5b2a33091861b1687e78ad23c7", + "Control_N1_mature.sorted.bam.bai:md5,01b52ea90bacac2ed44b4b165b03fe1f", + "Clone1_N1_mature.sorted.stats:md5,edfa6dab3271e66f743da2aca3ea7663", + "Clone9_N3_mature.sorted.bam:md5,d0fcf12036df675761eddb6e03eee657", + "Clone9_N3_mature.sorted.stats:md5,4fe47f64e7bdd0e1efeaa8271e92000a", + "Clone1_N1_mature.sorted.bam:md5,09f0d3c5b4e216d300904235fbb82494", + "Control_N1_mature.sorted.bam:md5,b2947881dd6b9631d701e175b7ac77e4", + "Control_N1_mature.sorted.stats:md5,9abec7b88211f78d0e743dbedb1e1125", + "Control_N1_mature.sorted.idxstats:md5,8e96945e95b03c3c33867c98dece1e4e", + "Clone9_N3_mature.sorted.idxstats:md5,f92b6bdb8bf206757d8e2733f60f3c1b", + "Clone9_N3_mature.sorted.flagstat:md5,bbb6bc880f6fc9424fc16b095af752b9", + "Clone9_N3_mature.sorted.bam.bai:md5,2504e62544b9f89fdbe2e8ad20b7e727", + "Clone1_N1_mature.sorted.bam.bai:md5,97c3b9ace9b0451ca7f6b9230e64bbfa", + "Clone1_N1_mature.sorted.idxstats:md5,f80f8349d8a814e8f67ef4c30e2f6a53", + "Clone1_N1_mature.sorted.flagstat:md5,e6adf8d4926033f9ae6a0d5ab42bd267", + "Control_N1_mature.sorted.flagstat:md5,f10e74138d682fed95c076112b7f9236", + "mirna.tsv:md5,b884a1dadb2a803fc3838f124695c68c", + "mirtop.tsv:md5,e82e7e158ad6541f7240d370c998b162", + "mirtop.gff:md5,e421a0dd1676ebdd331d4463fd7ec202", + "mirtop_rawData.tsv:md5,edae282cde52e6b60d42962479866cb3", + "mirtop_stats.txt:md5,3e59e311a62e873c7ec780d537d5e6a9", + "Control_N1.fastp_trimmed.fastq.gz:md5,8d0676323aa9e84556cdf209db92b6ed", + "Clone1_N1.fastp_trimmed.fastq.gz:md5,1ce9b5ab0591aa067c0bcfbc4852cd19", + "Clone9_N3.fastp_trimmed.fastq.gz:md5,abb626ba9f41ef35a3684d2b5b4f2c4f", + "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", + "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", + "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "mature_unmapped_read_counts.txt:md5,6f07c6c8054b843783c2b52888c12072", + "mature_normalized_CPM.txt:md5,025ac0731eb3817362983dcf6f3b4f79", + "hairpin_logtpm.csv:md5,4ac659c6e352ecd45970659eef009d33", + "mature_logtpm.txt:md5,9d0d4718cb7f72abbb26380745f42bc4", + "mature_edgeR_MDS_plot_coordinates.txt:md5,ef1fcf3b375b65c0611e32f1fa527759", + "hairpin_unmapped_read_counts.txt:md5,64a71970c8ebb5a7326f487c20685cee", + "mature_edgeR_MDS_distance_matrix.txt:md5,9b2553e2af74f3093386c88945d16514", + "mature_log2CPM_sample_distances.txt:md5,3e65534b731a92efdfe0373ff0b963ff", + "hairpin_log2CPM_sample_distances.txt:md5,2d89f929eff72230c1a6e8bffc8fa17a", + "hairpin_edgeR_MDS_distance_matrix.txt:md5,5001dc46960da9b83f7c528ad8116ddd", + "hairpin_logtpm.txt:md5,2bfc416b0011b131a5d2b8a4b8d3d7b5", + "hairpin_edgeR_MDS_plot_coordinates.txt:md5,f3ff4a57f6c4e8c9a3065c5fde85438b", + "mature_logtpm.csv:md5,2729c7b78855871f8b07804ab36ba8dd", + "hairpin_normalized_CPM.txt:md5,89c4abe13c09cd3e58b67a1e46e8e6e3", + "mature_counts.csv:md5,7714ee131dca993a1de82f22768db77d", + "hairpin_counts.csv:md5,55b0389a0a101bbf09a4718532f64514" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:39:11.127160605" + } +} \ No newline at end of file diff --git a/tests/test_umi.nf.test b/tests/test_umi.nf.test index 72a3deff..1901837d 100644 --- a/tests/test_umi.nf.test +++ b/tests/test_umi.nf.test @@ -1,4 +1,3 @@ - nextflow_pipeline { name "Test Workflow main.nf - test_umi" @@ -11,7 +10,7 @@ nextflow_pipeline { when { params { - outdir = "$outputDir" + outdir = "$outputDir" } } @@ -20,100 +19,162 @@ nextflow_pipeline { { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, { assert workflow.trace.succeeded().size() == 64 }, + + { assert snapshot( + path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.edited.fa"), + path("$outputDir/bowtie_index/genome/genome.3.ebwt"), + path("$outputDir/bowtie_index/genome/genome.4.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") + ).match("bowtie_index") }, + + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), + path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_contamination_check_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") + ).match("multiqc") }, + + { assert snapshot( + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam.bai"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats") + ).match("genome_quant") }, + + { assert snapshot( + path("$outputDir/umi_dedup/bam_deduplicated/SRX8195117_SRR11631013.umi_dedup.sorted.fastq.gz"), + path("$outputDir/umi_dedup/bam_deduplicated/SRX8195118_SRR11631014.umi_dedup.sorted.fastq.gz"), + path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195118_SRR11631014.umi_extract.fastq.gz"), + path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195117_SRR11631013.umi_extract.fastq.gz") + ).match("umi_dedup") }, + { assert snapshot( - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195118_SRR11631014_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195117_SRR11631013_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/SRX8195118_SRR11631014_seqcluster.bam"), path("$outputDir/mirna_quant/bam/seqcluster/SRX8195117_SRR11631013_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195118_SRR11631014_seqcluster_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/seqcluster/SRX8195118_SRR11631014_seqcluster.bam"), path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195117_SRR11631013_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195118_SRR11631014_seqcluster_unmapped.fq.gz"), path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.idxstats"), path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.idxstats"), path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.stats"), path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.bam"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.bam"), path("$outputDir/mirna_quant/bam/hairpin/unmapped/SRX8195118_SRR11631014_mature_hairpin_unmapped.fq.gz"), path("$outputDir/mirna_quant/bam/hairpin/unmapped/SRX8195117_SRR11631013_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/SRX8195118_SRR11631014.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam.bai"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.bam"), + path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195118_SRR11631014_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195117_SRR11631013_mature_unmapped.fq.gz"), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop.gff"), + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), path("$outputDir/mirna_quant/seqcluster/final/SRX8195117_SRR11631013.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv"), + path("$outputDir/mirna_quant/seqcluster/final/SRX8195118_SRR11631014.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.gff"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt") + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") ).match("mirna_quant") }, + { assert snapshot( - path("$outputDir/bowtie_index/genome/genome.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.3.ebwt"), - path("$outputDir/bowtie_index/genome/genome.4.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.edited.fa"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt") - ).match("bowtie_index") }, - { assert snapshot( - path("$outputDir/fastqc/raw/SRX8195118_SRR11631014.raw_fastqc.zip"), path("$outputDir/fastqc/raw/SRX8195117_SRR11631013.raw_fastqc.zip"), - path("$outputDir/fastqc/trimmed/SRX8195118_SRR11631014.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/SRX8195117_SRR11631013.trim_fastqc.zip") + path("$outputDir/fastqc/raw/SRX8195118_SRR11631014.raw_fastqc.zip"), + path("$outputDir/fastqc/trimmed/SRX8195117_SRR11631013.trim_fastqc.zip"), + path("$outputDir/fastqc/trimmed/SRX8195118_SRR11631014.trim_fastqc.zip") ).match("fastqc") }, + { assert snapshot( - path("$outputDir/umi_dedup/bam_deduplicated/SRX8195118_SRR11631014.umi_dedup.sorted.fastq.gz"), - path("$outputDir/umi_dedup/bam_deduplicated/SRX8195117_SRR11631013.umi_dedup.sorted.fastq.gz"), - path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195118_SRR11631014.umi_extract.fastq.gz"), - path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195117_SRR11631013.umi_extract.fastq.gz") - ).match("umi_dedup") }, - { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/SRX8195118_SRR11631014.fastp.fasta"), @@ -121,61 +182,7 @@ nextflow_pipeline { path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/SRX8195118_SRR11631014.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/SRX8195117_SRR11631013.fastp.fasta") ).match("mirtrace") }, - { assert snapshot( - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats") - ).match("genome_quant") }, - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_contamination_check_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt") - ).match("multiqc") }, + ) } diff --git a/tests/test_umi.nf.test.snap b/tests/test_umi.nf.test.snap new file mode 100644 index 00000000..2becd637 --- /dev/null +++ b/tests/test_umi.nf.test.snap @@ -0,0 +1,217 @@ +{ + "bowtie_index": { + "content": [ + "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", + "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", + "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", + "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", + "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", + "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", + "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", + "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", + "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", + "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", + "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", + "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", + "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", + "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", + "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", + "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", + "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", + "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", + "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:49:19.829287378" + }, + "mirtrace": { + "content": [ + "mirtrace-stats-rnatype.tsv:md5,00e584439bec82f5de8d6485a73dec37", + "mirtrace-stats-length.tsv:md5,3edbc31452dba97f8b829e3f8f635955", + "mirtrace-stats-contamination_detailed.tsv:md5,428d2fd6ea0a6f2af1018a557e89bece", + "mirtrace-stats-qcstatus.tsv:md5,de4f8a670b736bedf348d358cfdfb9fc", + "mirtrace-stats-contamination_basic.tsv:md5,3d54b37ab3206e9fec909fe3ea1a4777", + "mirtrace-stats-phred.tsv:md5,8cf9fc2223b9aeb50f92c8845edbf535", + "mirtrace-stats-mirna-complexity.tsv:md5,cd2f37963adeee159764a89688a4a6a5", + "SRX8195118_SRR11631014.fastp.fasta:md5,99e2ce92ce102bd3fedc3a9d3b926873", + "SRX8195117_SRR11631013.fastp.fasta:md5,e0e31d882568a7853dea75b3c595108f", + "SRX8195118_SRR11631014.fastp.fasta:md5,7db07b8c0b9e2b484eb3d42a04e480d1", + "SRX8195117_SRR11631013.fastp.fasta:md5,eb1ba9fa6f7d956e5d650fdd306d5634" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:49:46.029580614" + }, + "umi_dedup": { + "content": [ + "SRX8195117_SRR11631013.umi_dedup.sorted.fastq.gz:md5,247d78a2d700012064d0b2e28d04b061", + "SRX8195118_SRR11631014.umi_dedup.sorted.fastq.gz:md5,af2b98d9bd6d0760a7eb07813d015aee", + "SRX8195118_SRR11631014.umi_extract.fastq.gz:md5,d2928324ae465d3d8eaf65c24418b8cf", + "SRX8195117_SRR11631013.umi_extract.fastq.gz:md5,1aeed318fab39fa646ff790a025bd21d" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:49:20.579451915" + }, + "genome_quant": { + "content": [ + "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam.bai:md5,a2550ac81a655836969f91a4fbf64cf6", + "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats:md5,a4874de294706a7ead30258944ff2dad", + "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam:md5,b0534300df725919db7e38a8215d22b4", + "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam:md5,2dbac90f7439b878605b920ea7aa66a9", + "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats:md5,cc0413bf90252c3b3af8926fd64bc873", + "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat:md5,977e88cbe62027285df73e1f7f9cd9bc", + "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.flagstat:md5,235383f64a943885f5d899f5b8e03eba", + "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam.bai:md5,51444acc5b1c67d4bba3809a40e1ffd3", + "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats:md5,053912820064080299710bfbe7baf3c7", + "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats:md5,e19093f62044a7d053a0073092c506f3" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:49:20.293351627" + }, + "software_versions": { + "content": [ + "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTP_LENGTH_FILTER={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_GENOME={bowtie=1.3.1}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, UMICOLLAPSE_FASTQ={umicollapse=1.0.0-1}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:49:19.827254847" + }, + "fastqc": { + "content": [ + "SRX8195117_SRR11631013.raw_fastqc.zip:md5,26a041b01b10149a90a1a9233cb5cfd8", + "SRX8195118_SRR11631014.raw_fastqc.zip:md5,8a4b0ed8cf615100055caf5eb66afc9f", + "SRX8195117_SRR11631013.trim_fastqc.zip:md5,626143589a7acc028b2ecd01f687f03f", + "SRX8195118_SRR11631014.trim_fastqc.zip:md5,26ab263d79de53ded2eeb0d3a905f82e" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:49:36.864495018" + }, + "multiqc": { + "content": [ + "fastqc-status-check-heatmap.txt:md5,c1509fdd74b21a718fe099de64514995", + "fastp_filtered_reads_plot.txt:md5,3aaa79e1ede44347971c26100d9e954b", + "fastqc_top_overrepresented_sequences_table-1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "fastqc_sequence_counts_plot-1.txt:md5,24744e039ce4dbcbacf42edbfd642a8b", + "mirtrace_complexity_plot.txt:md5,5a860a872f793250b8c4482d031176a8", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,351f949c0abf4fb7587f3f5d9a28d461", + "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", + "samtools-stats-dp.txt:md5,74808822577fb62efb39811272e6919e", + "fastqc_sequence_length_distribution_plot.txt:md5,8c34b57ec084e2da9d62c254c0a517f4", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,dfdb23f41359b8a6b84d6626a0474d02", + "fastqc_sequence_duplication_levels_plot-1.txt:md5,b5ae95ecd73055798ed70947dda3747c", + "fastqc_per_base_sequence_quality_plot-1.txt:md5,89adfa92b1cde0ad4e401b430bbc68ce", + "multiqc_general_stats.txt:md5,b56535ef53b3ca4477aac99845712fa5", + "fastqc_per_base_n_content_plot-1.txt:md5,db081d3aa63007e5a78113f0fc26f27d", + "fastqc_per_base_n_content_plot.txt:md5,5b5b8cee3162d092c0bcddffbd000f34", + "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,66a47c7ce00ede2053f8e6eb20ec3417", + "fastqc_per_sequence_quality_scores_plot.txt:md5,3aa99649540afc898d32d2e49a364487", + "mirtrace_qc_plot.txt:md5,b08d11ea51c54e615f9608002644c787", + "fastqc_per_sequence_quality_scores_plot-1.txt:md5,4108da6fe352558a652ee2b17d609e07", + "mirtrace_length_plot.txt:md5,440a84ce9bbdb89b736e4e2446382665", + "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "fastqc-status-check-heatmap-1.txt:md5,cb2ea844834808ae4c95c6440269cf2e", + "fastqc_sequence_counts_plot.txt:md5,5e5c5132ff1969dfa40cb8b1eadf7a46", + "mirtrace_rna_categories_plot.txt:md5,6d08c297377a6241c4c1e82278d71f32", + "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,f36b7cfd3057b26281367397db45033a", + "samtools_alignment_plot.txt:md5,5e828961dbd55a6d6872221c49dfdc59", + "fastqc_per_base_sequence_quality_plot.txt:md5,e2e187bc0b0c1f0d1abb3b666945c7b3", + "mirtop_read_count_plot.txt:md5,2603cd59d95e71863e264ca9589591fa", + "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,bbad2035ada86867c4ed579a93b78d64", + "mirtop_unique_read_count_plot.txt:md5,5082d66ba230c780e87b78be589a2c3d", + "mirtop_mean_read_count_plot.txt:md5,5e2897fd0291f6e81a350786620f9b5a", + "mirtrace_contamination_check_plot.txt:md5,7f12917ce506127a729edb733fdda511", + "fastqc_adapter_content_plot.txt:md5,de1d7324ff5146b49fc9a2e6d4633962", + "fastqc_sequence_duplication_levels_plot.txt:md5,fe7598e49f93bb980a7675a2bb4bd3b5", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,c2f2f9282a50c3eef475664cc969b8ec", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,15d8fa32e0c11ef0d3d10fc28370972c", + "fastqc_adapter_content_plot-1.txt:md5,89cd342fdc6fbba5f67078c9a2f0c684", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,f832e92fb36db181ed1079be110edb2a", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,488e25de89d18d20f29b86f2580a8df9", + "multiqc_sources.txt:md5,e3350035ab949e3f5093d506077b0fe0", + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,d673e3b18c40c5af1edccffba386d678" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:49:20.057500216" + }, + "mirna_quant": { + "content": [ + "SRX8195117_SRR11631013_seqcluster.bam:md5,822cab8f3a85ddb27697cff48c702a2e", + "SRX8195118_SRR11631014_seqcluster.bam:md5,909d3ed731707db889ef6a2d1ca85aba", + "SRX8195117_SRR11631013_seqcluster_unmapped.fq.gz:md5,203db6b7864395ef7404e79d070a3ef4", + "SRX8195118_SRR11631014_seqcluster_unmapped.fq.gz:md5,c231087a920084e50ea28295e0af8797", + "SRX8195117_SRR11631013_mature_hairpin.sorted.idxstats:md5,4e7c1c98804febf6210cee5e3941709e", + "SRX8195118_SRR11631014_mature_hairpin.sorted.flagstat:md5,e0c44533bc7813d552de4864d997c916", + "SRX8195118_SRR11631014_mature_hairpin.sorted.idxstats:md5,f4485713620f31d97a5006acdf6d8a5d", + "SRX8195117_SRR11631013_mature_hairpin.sorted.stats:md5,b3ff5680bfebaaf6e30bb43a29a3031c", + "SRX8195117_SRR11631013_mature_hairpin.sorted.flagstat:md5,b86bd14dc687a26ba5a84d1015f4b70a", + "SRX8195118_SRR11631014_mature_hairpin.sorted.bam.bai:md5,5fb71506c8851af43d409ecd9fb1a13f", + "SRX8195118_SRR11631014_mature_hairpin.sorted.bam:md5,029b8b419ab9f61f6a45c00402ae4aa7", + "SRX8195117_SRR11631013_mature_hairpin.sorted.bam.bai:md5,82678a34d83ae306d0c6330c6b03b05a", + "SRX8195117_SRR11631013_mature_hairpin.sorted.bam:md5,4e047885963edc0e8848c68dcaaf28ec", + "SRX8195118_SRR11631014_mature_hairpin.bam:md5,4086b11369207f2ef469e52b59799d59", + "SRX8195118_SRR11631014_mature_hairpin.sorted.stats:md5,da76c29d304c53210242909c3e23a29a", + "SRX8195117_SRR11631013_mature_hairpin.bam:md5,ca5e172d1cb9dad640523a3fcf30cb7c", + "SRX8195118_SRR11631014_mature_hairpin_unmapped.fq.gz:md5,1a2c340984aa2e571b9cc2e7f4823356", + "SRX8195117_SRR11631013_mature_hairpin_unmapped.fq.gz:md5,b4402f45bb1984ed5f919d802df28fbd", + "SRX8195117_SRR11631013_mature.sorted.bam.bai:md5,d62ec895b633eea65fe783249aa4aaa7", + "SRX8195118_SRR11631014_mature.sorted.idxstats:md5,8b9cf0f1647b938f058b80522df24667", + "SRX8195117_SRR11631013_mature.sorted.bam:md5,5e20be9c8d3201b5ffa6eadbad06b699", + "SRX8195118_SRR11631014_mature.bam:md5,3ef1863216a59735fc12a258c847bebc", + "SRX8195117_SRR11631013_mature.sorted.flagstat:md5,171387fb18ba9868e28ca03d24a7daca", + "SRX8195118_SRR11631014_mature.sorted.stats:md5,bf67cbae75e68e5de07d042487010498", + "SRX8195118_SRR11631014_mature.sorted.flagstat:md5,57c6d477394d367ebae59f7267b430a5", + "SRX8195117_SRR11631013_mature.sorted.stats:md5,c5ed9f69f29172af201968f97b49be67", + "SRX8195118_SRR11631014_mature.sorted.bam:md5,d55bec2368640fede5da1704dbccfb94", + "SRX8195117_SRR11631013_mature.sorted.idxstats:md5,fb6c4000f82a66654b4f2a40570649b5", + "SRX8195118_SRR11631014_mature.sorted.bam.bai:md5,882a03bf714b0ba388496ef3b8df76e7", + "SRX8195117_SRR11631013_mature.bam:md5,125a84bae34979111a25f26e30c2a07e", + "SRX8195118_SRR11631014_mature_unmapped.fq.gz:md5,4d20ecfb8963b9ff1b03825dd3c4c365", + "SRX8195117_SRR11631013_mature_unmapped.fq.gz:md5,dab237af96d3d48d48168337e1aa117d", + "mirna.tsv:md5,e30f3037522a0a20f2a4b32cbb70990a", + "mirtop.tsv:md5,6c83e7efc40b4dc94d63259aa57b22c8", + "mirtop.gff:md5,29d876ccb32a8ed95da4ae8b6b1c08a7", + "mirtop_rawData.tsv:md5,ed4a0ceb2e8cd1721aa5ed27270f9623", + "mirtop_stats.txt:md5,9dcdf713a5096c123e32f7c2823c4451", + "SRX8195117_SRR11631013.fastp_trimmed.fastq.gz:md5,0a0da4dc5c49678d8421537dbf3067bc", + "SRX8195118_SRR11631014.fastp_trimmed.fastq.gz:md5,cf4de7d3978d5ff4709a88d3d2d034d8", + "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", + "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", + "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "mature_unmapped_read_counts.txt:md5,d2bc7fbe481ea26a72d7a5f35343fa8b", + "mature_normalized_CPM.txt:md5,57aa77072446dbaf32cbada7b085ee09", + "hairpin_logtpm.csv:md5,1435ade38403ded966117ba52bbbbaec", + "mature_logtpm.txt:md5,950dc03ce0c2e4e28fc6512aa307dcc2", + "hairpin_unmapped_read_counts.txt:md5,b6bf9d21c775ce6c9ef48a3d4ecf4d6b", + "hairpin_logtpm.txt:md5,0abfd7800b04a2b8fbe5ac8b683d6ca1", + "mature_logtpm.csv:md5,081545598a64d691050ebc0e52e783c0", + "hairpin_normalized_CPM.txt:md5,6176bf533f063247be51a02049e80add", + "mature_counts.csv:md5,dd82aef87b563b63c62cbab5a177025c", + "hairpin_counts.csv:md5,a7129322910eae9291d10820403a3491" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-19T21:49:27.68981406" + } +} \ No newline at end of file From f64efd0945922415d64c7b58dfc1776dd1773d5b Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Tue, 20 Aug 2024 19:55:36 +0000 Subject: [PATCH 04/15] Minimal profiles for testing ci settings --- .github/workflows/ci.yml | 85 ++---- tests/test.nf.test | 274 +------------------ tests/test.nf.test.snap | 319 ---------------------- tests/test_index.nf.test | 241 +--------------- tests/test_index.nf.test.snap | 292 -------------------- tests/test_mirgenedb.nf.test | 27 ++ tests/test_no_genome.nf.test | 272 +----------------- tests/test_no_genome.nf.test.snap | 311 --------------------- tests/test_technical_repeats.nf.test | 120 +------- tests/test_technical_repeats.nf.test.snap | 153 ----------- tests/test_umi.nf.test | 166 +---------- tests/test_umi.nf.test.snap | 217 --------------- 12 files changed, 51 insertions(+), 2426 deletions(-) delete mode 100644 tests/test.nf.test.snap delete mode 100644 tests/test_index.nf.test.snap create mode 100644 tests/test_mirgenedb.nf.test delete mode 100644 tests/test_no_genome.nf.test.snap delete mode 100644 tests/test_technical_repeats.nf.test.snap delete mode 100644 tests/test_umi.nf.test.snap diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c798356f..41843f15 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,53 +1,34 @@ name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: + push: + branches: + - dev pull_request: + release: + types: [published] env: NXF_ANSI_LOG: false - NFT_VER: "0.8.4" - NFT_WORKDIR: "~" - NFT_DIFF: "pdiff" - NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2" + CAPSULE_LOG: none + NFTEST_VER: "0.8.4" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" cancel-in-progress: true -jobs: - nf-test-changes: - name: Check for changes - runs-on: ubuntu-latest - outputs: - nf_test_files: ${{ steps.list.outputs.components }} - steps: - - uses: actions/checkout@v4 - with: - fetch-depth: 0 - - - name: List nf-test files - id: list - uses: adamrtalbot/detect-nf-test-changes@v0.0.2 - with: - head: ${{ github.sha }} - base: origin/${{ github.base_ref }} - include: .github/include.yaml - - - name: print list of nf-test files - run: | - echo ${{ steps.list.outputs.components }} +jobs: test: - name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }} - needs: [nf-test-changes] - if: needs.nf-test-changes.outputs.nf_test_files != '[]' + name: Run pipeline with test data + # Only run on push if this is the nf-core dev branch (merged PRs) + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/smrnaseq') }}" runs-on: ubuntu-latest strategy: fail-fast: false matrix: NXF_VER: + - "23.04.0" - "latest-everything" - - "23.04" - nf_test_files: ["${{ fromJson(needs.nf-test-changes.outputs.nf_test_files) }}"] profile: - "test" - "test_no_genome" @@ -64,53 +45,25 @@ jobs: with: version: "${{ matrix.NXF_VER }}" - - uses: actions/setup-python@v4 - with: - python-version: "3.11" - architecture: "x64" + - name: Disk space cleanup + uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - - name: Install pdiff to see diff between nf-test snapshots + - name: Install nf-test run: | - python -m pip install --upgrade pip - pip install pdiff - - - uses: nf-core/setup-nf-test@v1 + wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER + sudo mv nf-test /usr/local/bin/ - name: Run nf-test - run: | - nf-test test --verbose ${{ matrix.nf_test_files }} --profile "+${{ matrix.profile }}" --junitxml=test.xml --tap=test.tap - - - uses: pcolby/tap-summary@v1 - with: - path: >- - test.tap + run: nf-test test tests/${{ matrix.profile }}.nf.test --profile +docker --junitxml=test.xml - name: Output log on failure if: failure() run: | sudo apt install bat > /dev/null - batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log + batcat --decorations=always --color=always .nf-test/tests/*/output/pipeline_info/software_versions.yml - name: Publish Test Report uses: mikepenz/action-junit-report@v3 if: always() # always run even if the previous step fails with: report_paths: test.xml - - confirm-pass: - runs-on: ubuntu-latest - needs: [test] - if: always() - steps: - - name: All tests ok - if: ${{ !contains(needs.*.result, 'failure') }} - run: exit 0 - - name: One or more tests failed - if: ${{ contains(needs.*.result, 'failure') }} - run: exit 1 - - - name: debug-print - if: always() - run: | - echo "toJSON(needs) = ${{ toJSON(needs) }}" - echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" diff --git a/tests/test.nf.test b/tests/test.nf.test index 098e74d5..3d766b2b 100644 --- a/tests/test.nf.test +++ b/tests/test.nf.test @@ -18,279 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 196 }, - - { assert snapshot( - path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.edited.fa"), - path("$outputDir/bowtie_index/genome/genome.3.ebwt"), - path("$outputDir/bowtie_index/genome/genome.4.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, - - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") - ).match("multiqc") }, - - { assert snapshot( - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai") - ).match("genome_quant") }, - - { assert snapshot( - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.gff"), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") - ).match("mirna_quant") }, - - { assert snapshot( - path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip") - ).match("fastqc") }, - - { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") - ).match("mirtrace") }, - + { assert workflow.trace.succeeded().size() == 196 } ) } diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap deleted file mode 100644 index b26b2a15..00000000 --- a/tests/test.nf.test.snap +++ /dev/null @@ -1,319 +0,0 @@ -{ - "bowtie_index": { - "content": [ - "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", - "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", - "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", - "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", - "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", - "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", - "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", - "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", - "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", - "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", - "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", - "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", - "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", - "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", - "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", - "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", - "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", - "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", - "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:05:11.173010609" - }, - "mirtrace": { - "content": [ - "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", - "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", - "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", - "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", - "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", - "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", - "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638", - "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", - "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", - "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", - "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", - "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", - "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", - "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", - 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"Clone9_N3_mature.sorted.flagstat:md5,4f60cfd3527e91df204253f9f1aebfcd", - "Control_N3_mature.sorted.idxstats:md5,5fb7b46915043bd3c947a37afc3e8075", - "Clone9_N3_mature.sorted.bam.bai:md5,b1ac22e2ceb13f78bcede9cef82d2989", - "Clone1_N1_mature.sorted.bam.bai:md5,6b5783e42dca72415ed9cc25cd94b6cb", - "Clone1_N1_mature.sorted.idxstats:md5,77ed64ddd23cf07340b65c04559d4726", - "Control_N3_mature.sorted.bam:md5,9016fcda58013dedb5dea875cc718bd8", - "Clone1_N1_mature.sorted.flagstat:md5,f138a532bc7dab94f7cf4b4a4e5e23e5", - "Control_N3_mature.sorted.stats:md5,ff9dab4d3220aa44cdc80ea2fc311823", - "Clone1_N3_mature.sorted.stats:md5,e8feced949af44c8e5d31523b12122b9", - "Clone1_N3_mature.sorted.bam:md5,ffa1485c08ac5f4a2edebb88c892a7d6", - "Clone9_N1_mature.sorted.bam:md5,9fc8f4311a10f8ed65151017d861ab7f", - "Control_N1_mature.sorted.flagstat:md5,16318a574fe410b81c0e2cdf0dfa3c97", - "Clone9_N1_mature.sorted.stats:md5,02184884c17c8730f4df9e1a6144bbdc", - "mirna.tsv:md5,1f840afe7ab68eac73feaaad321b64f6", - "mirtop.tsv:md5,671628c0cf82376f674562ba1a6f6790", - "mirtop.gff:md5,598d14684b224dc897e3324448da2a7d", - "mirtop_rawData.tsv:md5,774410dd2cf1e5be83bf8d6e1e8b96b0", - "mirtop_stats.txt:md5,8b1ce9988d872c72ab3b23ed43000f7c", - "Clone1_N3.fastp_trimmed.fastq.gz:md5,2e395240c74b3870efe03dc329d8bad8", - "Control_N1.fastp_trimmed.fastq.gz:md5,2f09082eb68a8f1dc308050e330887ec", - "Control_N3.fastp_trimmed.fastq.gz:md5,342368a6e6acdaf0ae9379676b6d07f0", - "Clone9_N1.fastp_trimmed.fastq.gz:md5,115cf0c346a93a47ba782c5724b4f090", - "Clone1_N1.fastp_trimmed.fastq.gz:md5,14a2590e663dbde105780726c2173c25", - "Clone9_N2.fastp_trimmed.fastq.gz:md5,c922ec95a4b84d806dd2054ff0f9cab7", - "Clone9_N3.fastp_trimmed.fastq.gz:md5,67cf9a7d2fa431f0e772391ed1651f93", - "Control_N2.fastp_trimmed.fastq.gz:md5,d6e607edcb3d71c546ce8fdfb18e3999", - "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", - "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", - "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", - "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", - "mature_unmapped_read_counts.txt:md5,5673c4e9f6715d7ae7e137035e7e080e", - "mature_normalized_CPM.txt:md5,f6d11da1bb701b19780093094421c10e", - "hairpin_logtpm.csv:md5,923c8fff7480c89bcb18acfa2b398b4a", - "mature_logtpm.txt:md5,8851354ac087c8547aa9710eb49bc1d5", - "mature_edgeR_MDS_plot_coordinates.txt:md5,dfca9dca59af62be59bf43a10c9ee27e", - "hairpin_unmapped_read_counts.txt:md5,432fb18356e27c15569b62140f482435", - "mature_edgeR_MDS_distance_matrix.txt:md5,d386896da5ba156a76052895253f41c5", - "mature_log2CPM_sample_distances.txt:md5,bea4b11907cd6badbc68e9b505a48bb8", - "hairpin_log2CPM_sample_distances.txt:md5,b19fa1d9f821fc8e2c0e9f34f76b5479", - "hairpin_edgeR_MDS_distance_matrix.txt:md5,71074c2cb4661feaf822929250c8d3a9", - "hairpin_logtpm.txt:md5,d474bafadfed004173d15094ff6d4e25", - "hairpin_edgeR_MDS_plot_coordinates.txt:md5,666f384ea6cdd06a6140b8b9c8e2bb66", - "mature_logtpm.csv:md5,2ecf0babb4dfed8f25be9a40b953855d", - "hairpin_normalized_CPM.txt:md5,1c1104bda88b19465e890e8f7fdbac86", - "mature_counts.csv:md5,c006871cb0a4b01c47de2c0d8955fd0a", - "hairpin_counts.csv:md5,64d35f8b6fa3dfac237d944c1463cd03" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:05:15.071197394" - } -} \ No newline at end of file diff --git a/tests/test_index.nf.test b/tests/test_index.nf.test index 86e6b2f9..6996ff69 100644 --- a/tests/test_index.nf.test +++ b/tests/test_index.nf.test @@ -18,246 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 161 }, - - { assert snapshot( - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, - - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") - ).match("multiqc") }, - - { assert snapshot( - path("$outputDir/untar/bowtie_index/genome.rev.2.ebwt"), - path("$outputDir/untar/bowtie_index/genome.2.ebwt"), - path("$outputDir/untar/bowtie_index/genome.1.ebwt"), - path("$outputDir/untar/bowtie_index/genome.3.ebwt"), - path("$outputDir/untar/bowtie_index/genome.4.ebwt"), - path("$outputDir/untar/bowtie_index/genome.rev.1.ebwt") - ).match("untar") }, - - { assert snapshot( - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam") - ).match("genome_quant") }, - - { assert snapshot( - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.gff"), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") - ).match("mirna_quant") }, - - { assert snapshot( - path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip") - ).match("fastqc") }, - - { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") - ).match("mirtrace") }, - + { assert workflow.trace.succeeded().size() == 161 } ) } diff --git a/tests/test_index.nf.test.snap b/tests/test_index.nf.test.snap deleted file mode 100644 index f9fb5e9f..00000000 --- a/tests/test_index.nf.test.snap +++ /dev/null @@ -1,292 +0,0 @@ -{ - "bowtie_index": { - "content": [ - "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", - "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", - "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", - "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", - "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", - "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", - "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", - "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", - "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", - "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", - "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", - "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:14:50.023826353" - }, - "mirtrace": { - "content": [ - "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", - "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", - "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", - "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", - "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", - "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", - "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638", - "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", - "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", - "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", - "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", - "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", - "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", - "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", - "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8", - "Clone1_N1.fastp.fasta:md5,e297dfa46353946d6c140e4513dd4525", - "Clone9_N1.fastp.fasta:md5,63a17d136548fc98f34c8d98006cc7da", - "Control_N3.fastp.fasta:md5,d9980a598ece252e19d6c9ebefd51861", - "Control_N1.fastp.fasta:md5,e964e05ce2c93937a8e76602f2e08150", - "Clone9_N2.fastp.fasta:md5,b1ca39e6e1e75ee7d654d9ccfb35e906", - "Control_N2.fastp.fasta:md5,8cefbc494be7b363b19c10b8c00366b2", - "Clone1_N3.fastp.fasta:md5,4012282462dde0750f09cec883304cc3", - "Clone9_N3.fastp.fasta:md5,f733e20eb8d2a2009ca82464e8ccb148" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:15:11.764221931" - }, - "genome_quant": { - "content": [ - "Control_N2_mature_hairpin_genome.sorted.flagstat:md5,b0d42e94b2e0e026cd32a88dce40722c", - "Control_N2_mature_hairpin_genome.sorted.stats:md5,1222b755feaf406ecea3f2abb35a737c", - "Control_N2_mature_hairpin_genome.sorted.idxstats:md5,b6da32ce230fdeab39f3c4d5dcf41a3a", - "Control_N2_mature_hairpin_genome.sorted.bam.bai:md5,4052b95a49716e7f1b7309344bd01e67", - "Control_N2_mature_hairpin_genome.sorted.bam:md5,2dc37926d8badbbe3b88b24430f5be67" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:14:50.578371837" - }, - "software_versions": { - "content": [ - "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, UNTAR_BOWTIE_INDEX={untar=1.3}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:14:50.021513324" - }, - "fastqc": { - "content": [ - "Control_N1.raw_fastqc.zip:md5,81f40570d63474bcf55abda315e29c45", - "Clone9_N3.raw_fastqc.zip:md5,66cb401b11ae6813204606aeccf1b8c8", - "Clone9_N1.raw_fastqc.zip:md5,beeef245ec717610477b16e4641f84c7", - "Control_N3.raw_fastqc.zip:md5,38d38114fc7e4052ff55a2255e368e73", - "Clone1_N3.raw_fastqc.zip:md5,5e92a1505bd3e4fb16da4796121a20fb", - "Control_N2.raw_fastqc.zip:md5,14a252bb4fdd6e77afa93803e0ec55dd", - "Clone9_N2.raw_fastqc.zip:md5,441c1fff9495796fa9ad311ef2783ce0", - "Clone1_N1.raw_fastqc.zip:md5,2289535f7e4ad7e6fe40db782685f7d6", - "Control_N3.trim_fastqc.zip:md5,9d1ced8a86b9d4e4eef152e9108108b2", - "Clone9_N3.trim_fastqc.zip:md5,0395cef983e26ed88323abe68ecc3ab9", - "Clone9_N2.trim_fastqc.zip:md5,66ceb8ea7563c1e7bbcbc8c70049cf2f", - "Clone9_N1.trim_fastqc.zip:md5,ee1f6a9d7998e4ac56fb15d13e39f4d9", - "Clone1_N1.trim_fastqc.zip:md5,d492d242944b2d86790582f4e9a2d724", - "Control_N2.trim_fastqc.zip:md5,47220a78db4a3667190f0702f9ed01a0", - "Control_N1.trim_fastqc.zip:md5,5c8d7c4e206be9efb1b22a463441dd22", - "Clone1_N3.trim_fastqc.zip:md5,e255d55c6693f6891484c97c2b3a64b0" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:15:01.578725616" - }, - "untar": { - "content": [ - "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", - "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", - "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", - "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", - "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", - "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:14:50.348773909" - }, - "multiqc": { - "content": [ - "fastqc-status-check-heatmap.txt:md5,30f55902420433a11971d36956e8576e", - "fastp_filtered_reads_plot.txt:md5,0af4d3cfbf463f33b2b88cdfd69909ac", - "fastqc_overrepresented_sequences_plot.txt:md5,d861a4a956a3023efa19b1259d8665b2", - "fastqc_top_overrepresented_sequences_table-1.txt:md5,928ade897074cb3ad411bcd31f504dd2", - "fastqc_sequence_counts_plot-1.txt:md5,37d8ae6c5734eb2679e65e46c9af9101", - "mirtrace_complexity_plot.txt:md5,5f78d6f559a9642e68e1fd74ac2c11ca", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", - "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", - "samtools-stats-dp.txt:md5,0f88cdcc523ea239c2dd7e1e2decec36", - "fastqc_sequence_length_distribution_plot.txt:md5,13f72b3be854c74cd7b5176ca0583770", - "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,06a4162d4787883b1f39a1b9acb7bb91", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,6a0df664a369ee216412f0033ed3a042", - "multiqc_general_stats.txt:md5,5097cefe7b3b0d0503eacf9e81e9b51e", - "fastqc_per_base_n_content_plot-1.txt:md5,048e9b2293217ab8b47ba0113b83c76c", - "fastqc_per_base_n_content_plot.txt:md5,fb8a49467d1679dbf716e1f00c1f25e5", - "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,b1481a9fbf5ea541b39aed99b51d616f", - "fastqc_per_sequence_quality_scores_plot.txt:md5,38dbd6509de7f1beac17e44acb8336be", - "mirtrace_qc_plot.txt:md5,c436d017382baed6617fc3c1ad8ab41d", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,69f4459318311103fe71a5d1d3b2c076", - "mirtrace_length_plot.txt:md5,2366f10eb8bd3c32d2b35e2df20c786c", - "fastqc_top_overrepresented_sequences_table.txt:md5,9acec391e0a46858e110f5baa65fb0a9", - "fastqc_overrepresented_sequences_plot-1.txt:md5,1de000de50cc7516bb9d996def14c6eb", - "fastqc-status-check-heatmap-1.txt:md5,e64c353797e6dc057d10b3194ca6b20d", - "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", - "mirtrace_rna_categories_plot.txt:md5,8665376e2a123e1661f82cbbee54789f", - "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", - "samtools_alignment_plot.txt:md5,ac24d7f3bf5858e7550d2f93446137e1", - "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", - "mirtop_read_count_plot.txt:md5,29cce56b45edc10ff63badfa49eaf6b9", - "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", - "mirtop_unique_read_count_plot.txt:md5,b540743844ef0cdb81390b9db1d23afe", - "mirtop_mean_read_count_plot.txt:md5,837e240c5ecd10b95257e65fcd9f8393", - "fastqc_adapter_content_plot.txt:md5,86a0f478fd3e690ef5132d08bf4e7625", - "fastqc_sequence_duplication_levels_plot.txt:md5,88b0babe77f623547e8af664791ef2d0", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,539883757ae5bf731da93fe0568022e9", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,ed7205b9c46d5f431c5b3bf499a673a1", - "fastqc_adapter_content_plot-1.txt:md5,71ba0983a71f3a833526ab83a985d072", - "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,a8387a3e6b350acd16bb0ed5a43949d8", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3e9c1a7204c12d9c1b3b53342cf61840", - "multiqc_sources.txt:md5,d5202aca3585fa8914aa600bea4825e1", - "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,efa8123c9ad43f99a6fba671f50322ca" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:14:50.192712649" - }, - "mirna_quant": { - "content": [ - "Control_N1_mature_hairpin.sorted.stats:md5,feb69ad2f8bbc527e39502a297f08abd", - "Control_N1_mature_hairpin.sorted.idxstats:md5,e1f455195f1cb42a1d1e58770aaeb2b4", - "Clone1_N3_mature_hairpin.sorted.flagstat:md5,6f14ec4cd502c0eb213b1905b4568a76", - "Clone9_N2_mature_hairpin.sorted.stats:md5,7bb8654d44dac245aec6aa045250628a", - "Clone9_N3_mature_hairpin.sorted.flagstat:md5,efc65cb620ca139b19967e12f13ba007", - "Control_N1_mature_hairpin.sorted.bam.bai:md5,28b1225b55f40c3537de733de9a6768f", - "Control_N3_mature_hairpin.sorted.bam.bai:md5,c15c68783029019acf79b392384cf0b4", - "Control_N1_mature_hairpin.sorted.flagstat:md5,41769a400a176ea78432749f07f80fda", - "Control_N1_mature_hairpin.sorted.bam:md5,ff9eaccd9de8616315ac1cc19d01547a", - "Clone9_N1_mature_hairpin.sorted.stats:md5,155f327a9be0afa9584ec426826b5457", - "Clone1_N3_mature_hairpin.sorted.bam:md5,0468b44c0c5fa22a027cfc9abe8f0386", - "Control_N2_mature_hairpin.sorted.stats:md5,1195dd51f77e338db83dc66476ac7c5f", - "Clone9_N1_mature_hairpin.sorted.bam.bai:md5,b545947ebeb48b941a0ff77c463da13d", - "Control_N3_mature_hairpin.sorted.idxstats:md5,2c44710ce63bdebb12d64c729ef338b0", - "Control_N2_mature_hairpin.sorted.bam.bai:md5,fc6c5ea2d38928afad19a85ea7b51b47", - "Clone1_N3_mature_hairpin.sorted.bam.bai:md5,302937440b1786922a8f2d1659ba6a6e", - "Clone1_N1_mature_hairpin.sorted.idxstats:md5,0bca2d01f734128f3c11cf2697433048", - "Clone9_N3_mature_hairpin.sorted.idxstats:md5,9523d29d411c2efb0a1756355230fa98", - "Control_N2_mature_hairpin.sorted.idxstats:md5,8859b6e432cef8b24d5fb258a06aaabe", - "Clone9_N2_mature_hairpin.sorted.flagstat:md5,663ae0bb8b29d1e1c3d75ef5df1015a4", - "Clone9_N1_mature_hairpin.sorted.flagstat:md5,3e4b295b54df05c438603edaa53123b1", - "Control_N3_mature_hairpin.sorted.flagstat:md5,f3df866b94dc6ef355b01f22047aaf4f", - "Clone1_N1_mature_hairpin.sorted.bam.bai:md5,914846c8ffea1fa43a4799b8cc90ac1e", - "Clone1_N1_mature_hairpin.sorted.bam:md5,6a2302ef9acb50511e0894d7d94a7d38", - "Control_N3_mature_hairpin.sorted.bam:md5,8cf19f32d26228983c961c0d978358db", - "Clone9_N3_mature_hairpin.sorted.stats:md5,9f61c028bb1c92667e31093156ada662", - "Clone1_N1_mature_hairpin.sorted.stats:md5,bd02cb15e666054edecc89d392d72902", - "Clone9_N2_mature_hairpin.sorted.idxstats:md5,04b1c0ea4f133b5ee9086eec1f4077e7", - "Clone1_N3_mature_hairpin.sorted.stats:md5,471db325d8ccd1fe787b5dd91dccf487", - "Clone9_N3_mature_hairpin.sorted.bam.bai:md5,3b745be9c28f88bcacbf1da3eafd63ad", - "Control_N2_mature_hairpin.sorted.flagstat:md5,2605548b5ab1e6ad6b5cf88ea0030909", - "Clone9_N1_mature_hairpin.sorted.idxstats:md5,238b462a2418d545418c0b3a28029bdf", - "Clone9_N2_mature_hairpin.sorted.bam.bai:md5,420327a97d9178d89170a5611a02d827", - "Control_N3_mature_hairpin.sorted.stats:md5,2f2249c537451d1f72dfe298f16093ac", - "Clone9_N1_mature_hairpin.sorted.bam:md5,71333f26f0ac943ced66c9358e804158", - "Clone9_N2_mature_hairpin.sorted.bam:md5,53e1e9289d60fdd1d3b9820af5064dd3", - "Clone1_N1_mature_hairpin.sorted.flagstat:md5,8d0c785fec7b300200863c68b158444c", - "Control_N2_mature_hairpin.sorted.bam:md5,79a584d7c68f57697257cda41e6b6ccf", - "Clone9_N3_mature_hairpin.sorted.bam:md5,946f27f50f1658c64c2c222c2f37d2b8", - "Clone1_N3_mature_hairpin.sorted.idxstats:md5,5b6cd8d5784c387d2649f18499a17c6e", - "Control_N1_mature.sorted.bam.bai:md5,9ad0d0c840f6335ae7227cfdf03f714a", - "Clone1_N1_mature.sorted.stats:md5,9c42ffda181ca24ab076efc16fcfd4b3", - "Clone1_N3_mature.sorted.idxstats:md5,805f115ac4d9c8033908bafaba6c92fb", - "Clone9_N2_mature.sorted.stats:md5,fb8c403012481dafb895013c555f6d85", - "Control_N2_mature.sorted.stats:md5,ef5935898e3ca45d898053af335d1dfb", - "Control_N3_mature.sorted.flagstat:md5,2831f55bccbcf666d1c313ef377bcb30", - "Clone9_N3_mature.sorted.bam:md5,6a20122570543da6042a94fade945407", - "Clone9_N1_mature.sorted.bam.bai:md5,0d1a7dbe6e97f7fa4811790e6640c978", - "Clone9_N3_mature.sorted.stats:md5,23b012dd60ea6dcec5cedb5a73ffc792", - "Clone1_N1_mature.sorted.bam:md5,dc305cfe5c54b93e5b91b00dba676780", - "Clone1_N3_mature.sorted.flagstat:md5,67fc6ba8516d4e5b3ed2a62febc92f0a", - "Clone9_N1_mature.sorted.idxstats:md5,c6eb22f3ff675e422d065375279150b2", - "Control_N1_mature.sorted.bam:md5,1c6e2e02df78ae15c535726b448e3704", - "Control_N1_mature.sorted.stats:md5,b4ffb3a7623e32420def4d3470a326ab", - "Control_N1_mature.sorted.idxstats:md5,847bc5c6ef44e1f9754e47e648a5ef98", - "Clone9_N2_mature.sorted.flagstat:md5,247e02da50509fc1b3c5b35001922a8d", - "Control_N2_mature.sorted.flagstat:md5,c8742d1b49535ff815c2def66cba681e", - "Control_N2_mature.sorted.bam.bai:md5,01e9905b9d121d3c0341488bade69180", - "Control_N2_mature.sorted.bam:md5,57f6e91f83799f8b9cbc739a1a28ab78", - "Clone9_N2_mature.sorted.bam.bai:md5,a68809526ec55ae96f6eb62a170ac5ca", - "Control_N2_mature.sorted.idxstats:md5,12388de965d69b6102b62bc9cdf27e85", - "Control_N3_mature.sorted.bam.bai:md5,720f79c56ab38ba1ebafeb9c0fe5cf45", - "Clone9_N1_mature.sorted.flagstat:md5,014b846757652783ff3f954a966b8a1b", - "Clone9_N2_mature.sorted.bam:md5,d96c5b1d9f1111936037a605043becdf", - "Clone1_N3_mature.sorted.bam.bai:md5,567e08c765069502219a2bf080a84600", - "Clone9_N3_mature.sorted.idxstats:md5,dee54e8e22dfca24acc290bf89a05cd4", - "Clone9_N2_mature.sorted.idxstats:md5,c9643d610de2f4d449a876e41dcab872", - "Clone9_N3_mature.sorted.flagstat:md5,4f60cfd3527e91df204253f9f1aebfcd", - "Control_N3_mature.sorted.idxstats:md5,5fb7b46915043bd3c947a37afc3e8075", - "Clone9_N3_mature.sorted.bam.bai:md5,b1ac22e2ceb13f78bcede9cef82d2989", - "Clone1_N1_mature.sorted.bam.bai:md5,6b5783e42dca72415ed9cc25cd94b6cb", - "Clone1_N1_mature.sorted.idxstats:md5,77ed64ddd23cf07340b65c04559d4726", - "Control_N3_mature.sorted.bam:md5,19a7b1b8801094562492576c28ec33c7", - "Clone1_N1_mature.sorted.flagstat:md5,f138a532bc7dab94f7cf4b4a4e5e23e5", - "Control_N3_mature.sorted.stats:md5,ff9dab4d3220aa44cdc80ea2fc311823", - "Clone1_N3_mature.sorted.stats:md5,e8feced949af44c8e5d31523b12122b9", - "Clone1_N3_mature.sorted.bam:md5,6176d098a0384709aa5d3589258c701d", - "Clone9_N1_mature.sorted.bam:md5,7a1024fc323335f31ebc8297dd789fc2", - "Control_N1_mature.sorted.flagstat:md5,16318a574fe410b81c0e2cdf0dfa3c97", - "Clone9_N1_mature.sorted.stats:md5,02184884c17c8730f4df9e1a6144bbdc", - "mirna.tsv:md5,1f840afe7ab68eac73feaaad321b64f6", - "mirtop.tsv:md5,8401bbe98e85a6d8b1ab7466d2e178ac", - "mirtop.gff:md5,57cc78c6e20626b41ec833dda81c40d1", - "mirtop_rawData.tsv:md5,774410dd2cf1e5be83bf8d6e1e8b96b0", - "mirtop_stats.txt:md5,8b1ce9988d872c72ab3b23ed43000f7c", - "Clone1_N3.fastp_trimmed.fastq.gz:md5,2e395240c74b3870efe03dc329d8bad8", - "Control_N1.fastp_trimmed.fastq.gz:md5,2f09082eb68a8f1dc308050e330887ec", - "Control_N3.fastp_trimmed.fastq.gz:md5,342368a6e6acdaf0ae9379676b6d07f0", - "Clone9_N1.fastp_trimmed.fastq.gz:md5,115cf0c346a93a47ba782c5724b4f090", - "Clone1_N1.fastp_trimmed.fastq.gz:md5,14a2590e663dbde105780726c2173c25", - "Clone9_N2.fastp_trimmed.fastq.gz:md5,c922ec95a4b84d806dd2054ff0f9cab7", - "Clone9_N3.fastp_trimmed.fastq.gz:md5,67cf9a7d2fa431f0e772391ed1651f93", - "Control_N2.fastp_trimmed.fastq.gz:md5,d6e607edcb3d71c546ce8fdfb18e3999", - "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", - "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", - "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", - "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", - "mature_unmapped_read_counts.txt:md5,41348458c2a8874dcb8a82a30c3f0e43", - "mature_normalized_CPM.txt:md5,88c481df2e8b073ebfaf440620a2cd2a", - "hairpin_logtpm.csv:md5,87f2d92a9ca3ed5390b4cc903776fde4", - "mature_logtpm.txt:md5,c5cd8a9a2176af9d0f7759f92233929d", - "mature_edgeR_MDS_plot_coordinates.txt:md5,29584c2e2e2378a91e891a628f63a892", - "hairpin_unmapped_read_counts.txt:md5,7618d6bdc018e5712343bf4eb8d94fa4", - "mature_edgeR_MDS_distance_matrix.txt:md5,974273c499e26854e27c2cdbe9fa5f2c", - "mature_log2CPM_sample_distances.txt:md5,bea4b11907cd6badbc68e9b505a48bb8", - "hairpin_log2CPM_sample_distances.txt:md5,b19fa1d9f821fc8e2c0e9f34f76b5479", - "hairpin_edgeR_MDS_distance_matrix.txt:md5,c8377298e59143e17f9d0822c83059c3", - "hairpin_logtpm.txt:md5,96d146b5de6066b609b56a2344dfde67", - "hairpin_edgeR_MDS_plot_coordinates.txt:md5,dedaa69ffc330ce3b61593f2c58054e3", - "mature_logtpm.csv:md5,1a22f980708232227336118a8212fa32", - "hairpin_normalized_CPM.txt:md5,02e3803d5a9b0e2f4be94fac0cb94429", - "mature_counts.csv:md5,4d9f320ae04949cc0111bd90e2a2587d", - "hairpin_counts.csv:md5,fd30079c785a28327226d7c51b68b9cc" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:14:50.931370818" - } -} \ No newline at end of file diff --git a/tests/test_mirgenedb.nf.test b/tests/test_mirgenedb.nf.test new file mode 100644 index 00000000..19636057 --- /dev/null +++ b/tests/test_mirgenedb.nf.test @@ -0,0 +1,27 @@ +nextflow_pipeline { + + name "Test Workflow main.nf - test_mirgenedb" + script "main.nf" + profile "test_mirgenedb" + tag "test_mirgenedb" + tag "pipeline" + + test("test_mirgenedb") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert workflow.trace.succeeded().size() == 193 } + ) + } + + } + +} diff --git a/tests/test_no_genome.nf.test b/tests/test_no_genome.nf.test index 3b502706..2805ce3c 100644 --- a/tests/test_no_genome.nf.test +++ b/tests/test_no_genome.nf.test @@ -18,277 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 147 }, - - { assert snapshot( - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, - - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") - ).match("multiqc") }, - - { assert snapshot( - path("$outputDir/mirna_quant/bam/seqcluster/Control_N3_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N3_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Control_N1_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N2_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N3_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N1_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Control_N2_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N1_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N2_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N1_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N1_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N3_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N1_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N3_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N3_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N2_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N1_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N1_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N3_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N2_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N2_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N3_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N3_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N1_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N3_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N1_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N3_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone1_N1_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N1_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N2_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone1_N3_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N2_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.gff"), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") - ).match("mirna_quant") }, - - { assert snapshot( - path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip") - ).match("fastqc") }, - - { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") - ).match("mirtrace") }, - + { assert workflow.trace.succeeded().size() == 147 } ) } diff --git a/tests/test_no_genome.nf.test.snap b/tests/test_no_genome.nf.test.snap deleted file mode 100644 index 2e8a572d..00000000 --- a/tests/test_no_genome.nf.test.snap +++ /dev/null @@ -1,311 +0,0 @@ -{ - "bowtie_index": { - "content": [ - "fasta_bidx.3.ebwt:md5,cccaad86d0d5e5f3c1d4ca3a700ee980", - "fasta_bidx.1.ebwt:md5,9935201150ff358248380e07219fe093", - "fasta_bidx.rev.1.ebwt:md5,5e75ec9fb284ba316b3982a93f4ded49", - "fasta_bidx.rev.2.ebwt:md5,ba8e745f11b3d28240a78efd5bf2a7b0", - "fasta_bidx.4.ebwt:md5,96e2e8ec9f02d324d845e0708ff4b552", - "fasta_bidx.2.ebwt:md5,9cf18dd788535404d7fd6a62450d2ce0", - "fasta_bidx.3.ebwt:md5,a6d3abdddbf80cb9b2c97bbd7bc1f084", - "fasta_bidx.1.ebwt:md5,a2162fb747e95535ea5a67023b8961cf", - "fasta_bidx.rev.1.ebwt:md5,27578696198a61b0a3f783802823337e", - "fasta_bidx.rev.2.ebwt:md5,726c60d9a0108739ba9b61774bc39633", - "fasta_bidx.4.ebwt:md5,62e35549f28a1a85ccaf35858b1726aa", - "fasta_bidx.2.ebwt:md5,876ebed9375cda6f248dfc940308fa5e" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:24:10.78656165" - }, - "mirtrace": { - "content": [ - "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", - "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", - "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", - "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", - "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", - "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", - "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638", - "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", - "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", - "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", - "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", - "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", - "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", - "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", - "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8", - "Clone1_N1.fastp.fasta:md5,e297dfa46353946d6c140e4513dd4525", - "Clone9_N1.fastp.fasta:md5,63a17d136548fc98f34c8d98006cc7da", - "Control_N3.fastp.fasta:md5,d9980a598ece252e19d6c9ebefd51861", - "Control_N1.fastp.fasta:md5,e964e05ce2c93937a8e76602f2e08150", - "Clone9_N2.fastp.fasta:md5,b1ca39e6e1e75ee7d654d9ccfb35e906", - "Control_N2.fastp.fasta:md5,8cefbc494be7b363b19c10b8c00366b2", - "Clone1_N3.fastp.fasta:md5,4012282462dde0750f09cec883304cc3", - "Clone9_N3.fastp.fasta:md5,f733e20eb8d2a2009ca82464e8ccb148" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:26:58.977826663" - }, - "software_versions": { - "content": [ - "{BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:24:10.784750713" - }, - "fastqc": { - "content": [ - "Control_N1.raw_fastqc.zip:md5,af5b899930327b5cd9cca384a6e00f27", - "Clone9_N3.raw_fastqc.zip:md5,036432fce2449ab8ee8e88c5d94b6035", - "Clone9_N1.raw_fastqc.zip:md5,5e78e15fa5d55cfb37a0284faa348da6", - "Control_N3.raw_fastqc.zip:md5,d453f121f08bc460abeb7b750f7d4954", - "Clone1_N3.raw_fastqc.zip:md5,a2ff0ab9708f561c310e95831f5e4f6b", - "Control_N2.raw_fastqc.zip:md5,daf98d903972b1f8264a7769014e7c0a", - "Clone9_N2.raw_fastqc.zip:md5,dcf185d38fee5509b746e605297cdb56", - "Clone1_N1.raw_fastqc.zip:md5,f602c33309ec4a8f8e9954b2df4e1d17", - "Control_N3.trim_fastqc.zip:md5,bde0f1e858811e9d162b36efe62e4af6", - "Clone9_N3.trim_fastqc.zip:md5,4721668f47d2f6efaa98c51a6e5e32fc", - "Clone9_N2.trim_fastqc.zip:md5,ca65b8f3550be1d320f49efe3e220110", - "Clone9_N1.trim_fastqc.zip:md5,79a372ed09aa6953b70629c45c0c4a17", - "Clone1_N1.trim_fastqc.zip:md5,e43d7a6d56bfebffabdf6c7577f02b2d", - "Control_N2.trim_fastqc.zip:md5,77ef72e3a78cdba6eba5fdbadbdf2d0b", - "Control_N1.trim_fastqc.zip:md5,4945e909c01839cf5081913d49058b7c", - "Clone1_N3.trim_fastqc.zip:md5,9c70fbdc7fd6b97920a6c500cd647867" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:25:34.948370046" - }, - "multiqc": { - "content": [ - "fastqc-status-check-heatmap.txt:md5,30f55902420433a11971d36956e8576e", - "fastp_filtered_reads_plot.txt:md5,0af4d3cfbf463f33b2b88cdfd69909ac", - "fastqc_overrepresented_sequences_plot.txt:md5,d861a4a956a3023efa19b1259d8665b2", - "fastqc_top_overrepresented_sequences_table-1.txt:md5,1227a0557d97c2270bf535cf26c903e3", - "fastqc_sequence_counts_plot-1.txt:md5,37d8ae6c5734eb2679e65e46c9af9101", - "mirtrace_complexity_plot.txt:md5,5f78d6f559a9642e68e1fd74ac2c11ca", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", - "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", - "samtools-stats-dp.txt:md5,951e248c4dce68d25e14f0c79ef36e2e", - "fastqc_sequence_length_distribution_plot.txt:md5,13f72b3be854c74cd7b5176ca0583770", - "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,06a4162d4787883b1f39a1b9acb7bb91", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,6a0df664a369ee216412f0033ed3a042", - "multiqc_general_stats.txt:md5,b87104303b78cbe5701807b79fa4c2b6", - "fastqc_per_base_n_content_plot-1.txt:md5,048e9b2293217ab8b47ba0113b83c76c", - "fastqc_per_base_n_content_plot.txt:md5,fb8a49467d1679dbf716e1f00c1f25e5", - "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,b1481a9fbf5ea541b39aed99b51d616f", - "fastqc_per_sequence_quality_scores_plot.txt:md5,38dbd6509de7f1beac17e44acb8336be", - "mirtrace_qc_plot.txt:md5,c436d017382baed6617fc3c1ad8ab41d", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,69f4459318311103fe71a5d1d3b2c076", - "mirtrace_length_plot.txt:md5,2366f10eb8bd3c32d2b35e2df20c786c", - "fastqc_top_overrepresented_sequences_table.txt:md5,9acec391e0a46858e110f5baa65fb0a9", - "fastqc_overrepresented_sequences_plot-1.txt:md5,1de000de50cc7516bb9d996def14c6eb", - "fastqc-status-check-heatmap-1.txt:md5,e64c353797e6dc057d10b3194ca6b20d", - "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", - "mirtrace_rna_categories_plot.txt:md5,8665376e2a123e1661f82cbbee54789f", - "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", - "samtools_alignment_plot.txt:md5,e4335c4194bffb41df16619f3abfe705", - "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", - "mirtop_read_count_plot.txt:md5,b50c5023f6ac2b30ed58395f5b7b67b8", - "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", - "mirtop_unique_read_count_plot.txt:md5,239a293d6a9c55159bc855c196cc2ca8", - "mirtop_mean_read_count_plot.txt:md5,68585c6d196e7a83800f29325590867c", - "fastqc_adapter_content_plot.txt:md5,86a0f478fd3e690ef5132d08bf4e7625", - "fastqc_sequence_duplication_levels_plot.txt:md5,88b0babe77f623547e8af664791ef2d0", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,539883757ae5bf731da93fe0568022e9", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,ed7205b9c46d5f431c5b3bf499a673a1", - "fastqc_adapter_content_plot-1.txt:md5,71ba0983a71f3a833526ab83a985d072", - "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,a8387a3e6b350acd16bb0ed5a43949d8", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3e9c1a7204c12d9c1b3b53342cf61840", - "multiqc_sources.txt:md5,74a9b42fd856cc0b715a2ce57644394d", - "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,efa8123c9ad43f99a6fba671f50322ca" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:24:10.944335466" - }, - "mirna_quant": { - "content": [ - "Control_N3_seqcluster.bam:md5,c90aa20f909ddf13059d95ab9d93b890", - "Clone9_N3_seqcluster.bam:md5,2a5d700e8ee076eb9de28de3def98e1f", - "Control_N1_seqcluster.bam:md5,142c18d8f4803e984d6caae2a76cd297", - "Clone9_N2_seqcluster.bam:md5,1e3e8a63eb9ed4e6a7ff37abbd7d1316", - "Clone1_N3_seqcluster.bam:md5,58d778be4b8614f9149c6dd9e381a603", - "Clone1_N1_seqcluster.bam:md5,2bccd1a3e26f136e0f6aa8e670656adc", - "Control_N2_seqcluster.bam:md5,0935caa87feade13d2faa1c4588e81e9", - "Clone9_N1_seqcluster.bam:md5,7c28dd875d3389b8d9804dfb53d2bc95", - "Clone9_N2_seqcluster_unmapped.fq.gz:md5,3573d4087ae030ba8e89810f54899dd6", - "Clone9_N1_seqcluster_unmapped.fq.gz:md5,c78a081ae80d643db179236fb2fb34e5", - "Clone1_N1_seqcluster_unmapped.fq.gz:md5,5f9c53a480254f93842e1452fb3bf730", - "Clone1_N3_seqcluster_unmapped.fq.gz:md5,baebce4abaf618377881af129f473464", - "Control_N1_seqcluster_unmapped.fq.gz:md5,e08c8237c239259854f5a38f34ce81e8", - "Clone9_N3_seqcluster_unmapped.fq.gz:md5,61074c6fdbaa5af136afd7c73dca4bd4", - "Control_N3_seqcluster_unmapped.fq.gz:md5,ec7a957d4289c4b28c4b9cf50d888501", - "Control_N2_seqcluster_unmapped.fq.gz:md5,53456f132a72635fadf487fac4419153", - "Control_N1_mature_hairpin.sorted.stats:md5,9eb22683401f87e60cbc0cc73b39b8b7", - "Control_N1_mature_hairpin.sorted.idxstats:md5,6ed8ee411919ec9baa5034679be63770", - "Clone1_N3_mature_hairpin.sorted.flagstat:md5,40449964287854e14984545f4007677c", - "Clone9_N2_mature_hairpin.sorted.stats:md5,925c282fdcd53d9b16e3c89840506daa", - "Control_N1_mature_hairpin.bam:md5,1365fa1eecd5f9240e4cd441301e9596", - "Clone9_N3_mature_hairpin.sorted.flagstat:md5,43adb927ee6032297e95fedc5b080ca1", - "Control_N1_mature_hairpin.sorted.bam.bai:md5,92a4a16cc5f31db1d380fc3e94791f56", - "Control_N3_mature_hairpin.sorted.bam.bai:md5,e824e1333610d606e6b85a87950050a2", - "Control_N3_mature_hairpin.bam:md5,e8d6747971e13255bc3d90d66c077220", - "Control_N1_mature_hairpin.sorted.flagstat:md5,94856ef0ef3e2944df1bddc31a118121", - "Control_N1_mature_hairpin.sorted.bam:md5,cc95e8f4d2e0430ea3e38916dc7177ad", - "Clone9_N1_mature_hairpin.sorted.stats:md5,fa18dddebf8b084542858f2c13342c2d", - "Clone1_N3_mature_hairpin.sorted.bam:md5,1bfce4322589920b4ba4cb53ed092b7b", - "Control_N2_mature_hairpin.sorted.stats:md5,0f618f0e64bd16ed4858c9012b7adf87", - "Clone9_N1_mature_hairpin.sorted.bam.bai:md5,3665f6fcfe9a3170319a4693e334aa92", - "Control_N3_mature_hairpin.sorted.idxstats:md5,0981f7a524ff0036b2d77c97147f0f0e", - "Clone9_N2_mature_hairpin.bam:md5,05a1018e4919645b660f2fd02eb7de79", - "Control_N2_mature_hairpin.sorted.bam.bai:md5,241f09f8545749940f75e01980c4a502", - "Clone1_N3_mature_hairpin.sorted.bam.bai:md5,f70574011e86510a9b4c03f0503e2308", - "Clone1_N1_mature_hairpin.sorted.idxstats:md5,d54f57a896c7b7b5824e3af5b51f3fd2", - "Clone9_N3_mature_hairpin.sorted.idxstats:md5,361861d00aa0086eb1aa8bacc616db60", - "Control_N2_mature_hairpin.bam:md5,9627e1986187feb8c29f25b1f601db0f", - "Control_N2_mature_hairpin.sorted.idxstats:md5,364ab0efe73b5369e362bf12ed738009", - "Clone9_N2_mature_hairpin.sorted.flagstat:md5,5f3be7d1cf5db0ac22b1e4bbbc89460f", - "Clone1_N3_mature_hairpin.bam:md5,070957bddc0ce7783268e642b3989b23", - "Clone9_N1_mature_hairpin.sorted.flagstat:md5,718c6b942e1171211326118f4877c4ad", - "Clone9_N3_mature_hairpin.bam:md5,fc047c063574735570f42ee15c07232d", - "Control_N3_mature_hairpin.sorted.flagstat:md5,dca2071057d621f04d3c88c5fcc061eb", - "Clone1_N1_mature_hairpin.sorted.bam.bai:md5,8cdbd05dd732977402fd76562b0efe00", - "Clone9_N1_mature_hairpin.bam:md5,3aea05b4086bc12c6dae8d9e592f7dd5", - "Clone1_N1_mature_hairpin.sorted.bam:md5,ed11e3eaeec16a0b8731876d04f9e85d", - "Control_N3_mature_hairpin.sorted.bam:md5,a6fb117e72ec854b6923c85a84ea6601", - "Clone9_N3_mature_hairpin.sorted.stats:md5,e414a9e5b8a6e737cdd5aacaaaa40da8", - "Clone1_N1_mature_hairpin.sorted.stats:md5,15987963f6d2a224565663ae49a2bb19", - "Clone9_N2_mature_hairpin.sorted.idxstats:md5,416c4f9aef6f2c79c329f477044e6485", - "Clone1_N3_mature_hairpin.sorted.stats:md5,8f0cb54dcf9604c6ea3cfc860b483725", - "Clone9_N3_mature_hairpin.sorted.bam.bai:md5,6878dfeb546c81a8a729f658d17b2c6f", - "Control_N2_mature_hairpin.sorted.flagstat:md5,886085252cd07b0bbe8073be4549c719", - "Clone9_N1_mature_hairpin.sorted.idxstats:md5,2c376fd533eaa5bfd321657e8cdfc9f1", - "Clone9_N2_mature_hairpin.sorted.bam.bai:md5,22cb9d52da218bae97710d42ff3142e1", - "Control_N3_mature_hairpin.sorted.stats:md5,55cac79ae09a6147ffba190d6115bfa4", - "Clone9_N1_mature_hairpin.sorted.bam:md5,f8be17f518dc9b7af0c5c33fbc543b3e", - "Clone9_N2_mature_hairpin.sorted.bam:md5,c34bc408ec180d49ebadfbcfabbf07a6", - "Clone1_N1_mature_hairpin.sorted.flagstat:md5,b2e8eb3b3d10a01a3794e2410c3ba270", - "Control_N2_mature_hairpin.sorted.bam:md5,ddc5d52a3cce2eac8a0157ad35df4f8b", - "Clone1_N1_mature_hairpin.bam:md5,99e73f811e024126e48e60dd50c44ae7", - "Clone9_N3_mature_hairpin.sorted.bam:md5,36132af606f4dd66a69a93ca20dd2fc8", - "Clone1_N3_mature_hairpin.sorted.idxstats:md5,a2457f5571563ecc03c4d9834fa75da0", - "Clone9_N1_mature_hairpin_unmapped.fq.gz:md5,2f0664e028c76f624d95af52df5b9988", - "Clone1_N1_mature_hairpin_unmapped.fq.gz:md5,77a17714c20e52c8f7a3a4a5b85c2cb3", - "Clone1_N3_mature_hairpin_unmapped.fq.gz:md5,901909393df6f5a36e13544f3e856aff", - "Clone9_N2_mature_hairpin_unmapped.fq.gz:md5,842987019b7ee22e0b3c3e454dad090f", - "Control_N2_mature_hairpin_unmapped.fq.gz:md5,984f690e586f2066fd3959bb26e1b2a9", - "Control_N3_mature_hairpin_unmapped.fq.gz:md5,50f499525a898e9145f9aad2d70bbed7", - "Clone9_N3_mature_hairpin_unmapped.fq.gz:md5,ea15bcefa3a9a69d4c22bb555f672851", - "Control_N1_mature_hairpin_unmapped.fq.gz:md5,2a0cda6eb6fb2cd06304fd69a4483dec", - "Control_N3_mature.bam:md5,75ca5d98d0aaaa9d693c56d90de1a045", - "Control_N1_mature.sorted.bam.bai:md5,187f273f39c4459cc6dae5dbe6943a84", - "Clone1_N1_mature.sorted.stats:md5,9c42ffda181ca24ab076efc16fcfd4b3", - "Clone1_N3_mature.sorted.idxstats:md5,39e30f2f398992208a5411c74a3c9774", - "Clone9_N2_mature.sorted.stats:md5,fb8c403012481dafb895013c555f6d85", - "Control_N2_mature.sorted.stats:md5,958b7a9ccfe3893b117317d00cd29949", - "Control_N3_mature.sorted.flagstat:md5,2831f55bccbcf666d1c313ef377bcb30", - "Clone9_N3_mature.sorted.bam:md5,1a1d3c718b2d61ff0df5af08b3a270b8", - "Clone9_N1_mature.sorted.bam.bai:md5,792064a331dcee563f2c9d89131257fc", - "Control_N2_mature.bam:md5,6b8bbe7b346e16738fb3054d7aff1d6d", - "Clone9_N3_mature.sorted.stats:md5,23b012dd60ea6dcec5cedb5a73ffc792", - "Clone1_N1_mature.sorted.bam:md5,94f2c8de0d832e161603ac13c04a80dc", - "Clone1_N3_mature.sorted.flagstat:md5,67fc6ba8516d4e5b3ed2a62febc92f0a", - "Clone9_N1_mature.sorted.idxstats:md5,4f5c53b3acc6ee228d5f5766bb4bf1d4", - "Control_N1_mature.sorted.bam:md5,b1f791c7c05ed79a7e0dcecd621ffb98", - "Control_N1_mature.sorted.stats:md5,b4ffb3a7623e32420def4d3470a326ab", - "Control_N1_mature.sorted.idxstats:md5,ec6150327db493da8faaca1525afacd1", - "Clone9_N2_mature.sorted.flagstat:md5,247e02da50509fc1b3c5b35001922a8d", - "Control_N2_mature.sorted.flagstat:md5,cdeb62c8bd17760b6d258a17bec1e80c", - "Clone1_N1_mature.bam:md5,a4bdd9fe63b0c46558785803c8a2c38a", - "Control_N2_mature.sorted.bam.bai:md5,6099ef1e91998df723db75f4f310a0a7", - "Control_N2_mature.sorted.bam:md5,77ca8d740b118d54396d811aea35aa25", - "Clone9_N2_mature.sorted.bam.bai:md5,dccf48ac51c38a86e54e7a7e8de442ab", - "Control_N2_mature.sorted.idxstats:md5,af6ecc38643b1aedf67354e91e95364e", - "Control_N3_mature.sorted.bam.bai:md5,ec26ee658ce263355991aa9b270fe8bb", - "Clone9_N1_mature.sorted.flagstat:md5,014b846757652783ff3f954a966b8a1b", - "Clone9_N2_mature.sorted.bam:md5,b3fd17a677e4b542217d011c54a3b825", - "Clone1_N3_mature.sorted.bam.bai:md5,4a9bef5bdb5e80d47f5d67a8860e3160", - "Clone9_N3_mature.sorted.idxstats:md5,84784ae05dce03ca691f7ae0b4074eb3", - "Clone1_N3_mature.bam:md5,e5898ea3b269fec3e0bd84671a8bcd8d", - "Clone9_N2_mature.sorted.idxstats:md5,1ecdffcf833b08768c83bd74bf5e1a95", - "Clone9_N3_mature.bam:md5,7246c160a0e78d0d0ee06ebfbda26877", - "Clone9_N3_mature.sorted.flagstat:md5,4f60cfd3527e91df204253f9f1aebfcd", - "Control_N3_mature.sorted.idxstats:md5,a38cb5edff03d442729ad3ab2dad5425", - "Control_N1_mature.bam:md5,9704faaff4a86e380e0c882099c73dc1", - "Clone9_N3_mature.sorted.bam.bai:md5,1e1d39c7abe355e3cecbbb4fc2173d94", - "Clone1_N1_mature.sorted.bam.bai:md5,5c3f93a439aee824b63756b6d3281acb", - "Clone1_N1_mature.sorted.idxstats:md5,69adbd609e315faaa5b03082919c941f", - "Control_N3_mature.sorted.bam:md5,f76a7e2f9c398ed662f9c1e58d095025", - "Clone1_N1_mature.sorted.flagstat:md5,f138a532bc7dab94f7cf4b4a4e5e23e5", - "Control_N3_mature.sorted.stats:md5,ff9dab4d3220aa44cdc80ea2fc311823", - "Clone9_N2_mature.bam:md5,6c35427293dd2ece2c95b81dad913ad8", - "Clone1_N3_mature.sorted.stats:md5,e8feced949af44c8e5d31523b12122b9", - "Clone1_N3_mature.sorted.bam:md5,a760ed85ecc686e3f84f7ff16ed924ef", - "Clone9_N1_mature.sorted.bam:md5,8af13c91caa7493b4f07d2d412f5548c", - "Clone9_N1_mature.bam:md5,f5e4c52412c28c222113010879993235", - "Control_N1_mature.sorted.flagstat:md5,16318a574fe410b81c0e2cdf0dfa3c97", - "Clone9_N1_mature.sorted.stats:md5,02184884c17c8730f4df9e1a6144bbdc", - "Control_N3_mature_unmapped.fq.gz:md5,7342270d6c56f5963975616dfbd1ea7b", - "Control_N1_mature_unmapped.fq.gz:md5,d3619daf05993c74778b56124a1c9b0b", - "Clone9_N3_mature_unmapped.fq.gz:md5,96963c170975470e839ee12287406b6f", - "Clone1_N1_mature_unmapped.fq.gz:md5,ba4ccae731a04630b51e2357f8eee62a", - "Clone9_N1_mature_unmapped.fq.gz:md5,d59e0d22095886c30c79a7e440d2181f", - "Clone9_N2_mature_unmapped.fq.gz:md5,a0bd26697f8745406bfe97b5c34985e8", - "Clone1_N3_mature_unmapped.fq.gz:md5,4b2e947182f383eed7a742fbb0cb7fb4", - "Control_N2_mature_unmapped.fq.gz:md5,4d6e259f01d963365ed90862c16ab473", - "mirna.tsv:md5,01179dda321cf235df8c1fb72609ecb4", - "mirtop.tsv:md5,544a9859d5cfb8083fdea86f36ecd7af", - "mirtop.gff:md5,f6220d75e81e67be3fbbd0251ce2947b", - "mirtop_rawData.tsv:md5,98c46ade3ba0b141f1306c1dbc9a3ff1", - "mirtop_stats.txt:md5,b28c2f920f1e73f827f32fdd31654cbd", - "Clone1_N3.fastp_trimmed.fastq.gz:md5,2e395240c74b3870efe03dc329d8bad8", - "Control_N1.fastp_trimmed.fastq.gz:md5,2f09082eb68a8f1dc308050e330887ec", - "Control_N3.fastp_trimmed.fastq.gz:md5,342368a6e6acdaf0ae9379676b6d07f0", - "Clone9_N1.fastp_trimmed.fastq.gz:md5,115cf0c346a93a47ba782c5724b4f090", - "Clone1_N1.fastp_trimmed.fastq.gz:md5,14a2590e663dbde105780726c2173c25", - "Clone9_N2.fastp_trimmed.fastq.gz:md5,c922ec95a4b84d806dd2054ff0f9cab7", - "Clone9_N3.fastp_trimmed.fastq.gz:md5,67cf9a7d2fa431f0e772391ed1651f93", - "Control_N2.fastp_trimmed.fastq.gz:md5,d6e607edcb3d71c546ce8fdfb18e3999", - "hairpin.fa_igenome.fa_idx.fa:md5,f7ee61ca4537300386fdb85c7dec24d2", - "mature.fa_igenome.fa_idx.fa:md5,48215f56ca0bfbdbb1a28482457283e3", - "hairpin.fa_igenome.fa:md5,cddcc379892cb43e807ff54feafafbc1", - "mature.fa_igenome.fa:md5,48215f56ca0bfbdbb1a28482457283e3", - "mature_unmapped_read_counts.txt:md5,edc81b30c58368abb964fe13310f9c04", - "mature_normalized_CPM.txt:md5,d8d8712785f930456e8e739c4081ccbb", - "hairpin_logtpm.csv:md5,2d1c128288f7d8aa8ea870d488fb0586", - "mature_logtpm.txt:md5,b47a967bbd764361beffe188ae31d278", - "mature_edgeR_MDS_plot_coordinates.txt:md5,af754c03339430a71c0998d8f0580e68", - "hairpin_unmapped_read_counts.txt:md5,b81d5b91da9af7eb747ab8b6a9243e26", - "mature_edgeR_MDS_distance_matrix.txt:md5,18533a2afb0a6fad6be1d879690111f7", - "mature_log2CPM_sample_distances.txt:md5,980bba51cd88ae0c8ac418fe653492af", - "hairpin_log2CPM_sample_distances.txt:md5,7cca5268281ff6e24f849526589b9e48", - "hairpin_edgeR_MDS_distance_matrix.txt:md5,fcd5a68b940856b28eac2ea029f61967", - "hairpin_logtpm.txt:md5,912a1604f482d5b4bb54199b0f07c6eb", - "hairpin_edgeR_MDS_plot_coordinates.txt:md5,cbef839bb66d6e832243df2bd46d4ebd", - "mature_logtpm.csv:md5,120c6af7180855ba68098685ca81c392", - "hairpin_normalized_CPM.txt:md5,47a03cbecaf025fdcebdb17148ace558", - "mature_counts.csv:md5,2ffb977afc7b61a79056c2868cd53222", - "hairpin_counts.csv:md5,118236c7fa7b56fa78e495582eaf285d" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:24:11.083677532" - } -} \ No newline at end of file diff --git a/tests/test_technical_repeats.nf.test b/tests/test_technical_repeats.nf.test index 22f5accf..f01233aa 100644 --- a/tests/test_technical_repeats.nf.test +++ b/tests/test_technical_repeats.nf.test @@ -18,125 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 75 }, - - { assert snapshot( - path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.edited.fa"), - path("$outputDir/bowtie_index/genome/genome.3.ebwt"), - path("$outputDir/bowtie_index/genome/genome.4.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, - - { assert snapshot( - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai") - ).match("genome_quant") }, - - { assert snapshot( - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.gff"), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") - ).match("mirna_quant") }, - - { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") - ).match("mirtrace") }, - + { assert workflow.trace.succeeded().size() == 75 } ) } diff --git a/tests/test_technical_repeats.nf.test.snap b/tests/test_technical_repeats.nf.test.snap deleted file mode 100644 index f18a5b4c..00000000 --- a/tests/test_technical_repeats.nf.test.snap +++ /dev/null @@ -1,153 +0,0 @@ -{ - "bowtie_index": { - "content": [ - "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", - "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", - "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", - "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", - "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", - "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", - "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", - "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", - "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", - "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", - "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", - "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", - "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", - "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", - "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", - "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", - "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", - "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", - "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:39:09.347754579" - }, - "mirtrace": { - "content": [ - "mirtrace-stats-rnatype.tsv:md5,2843855add34a73acd332a112bd80a34", - "mirtrace-stats-length.tsv:md5,71591c754eed9db419b91fb499f8e2ab", - "mirtrace-stats-contamination_detailed.tsv:md5,c16e27cc433dacdd5bfff09a9aaab736", - "mirtrace-stats-qcstatus.tsv:md5,37465e5d4d756792b95f187e6406fc6b", - "mirtrace-stats-contamination_basic.tsv:md5,ca3f99b1b89d2674864b62bbf9c41592", - "mirtrace-stats-phred.tsv:md5,1ac6fdae848cc4e39904edc361f75d1f", - "mirtrace-stats-mirna-complexity.tsv:md5,c69c4762a887a8e792c896dc5d3866b8", - "Clone1_N1.fastp.fasta:md5,7630d5d8f047d2f7e9492598e6f97c84", - "Control_N1.fastp.fasta:md5,534de89c8354a874458497804dcb7785", - "Clone9_N3.fastp.fasta:md5,0f2ef6c209a0b591d4eff5d77b713957", - "Clone1_N1.fastp.fasta:md5,f49d63f3d05aeb349f58f2bb95552332", - "Control_N1.fastp.fasta:md5,b34c20e0736351db5d0d1d3236de18ec", - "Clone9_N3.fastp.fasta:md5,726d1d14a88d7b816bb97bab9f006c45" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:39:17.175802364" - }, - "genome_quant": { - "content": [ - "Control_N1_mature_hairpin_genome.sorted.flagstat:md5,41e0b4dc62f9b8779534d67630ea6ab6", - "Clone9_N3_mature_hairpin_genome.sorted.stats:md5,872a90aca4d070f9403ae86b42666e2c", - "Clone9_N3_mature_hairpin_genome.sorted.flagstat:md5,50eb08817350b22dbe99bcc3dc7f2a38", - "Clone1_N1_mature_hairpin_genome.sorted.flagstat:md5,1d56901f0754350ee0925cff76bee6d1", - "Clone1_N1_mature_hairpin_genome.sorted.bam:md5,aee26f20d3188c9e0c17c8b19ee01068", - "Clone1_N1_mature_hairpin_genome.sorted.bam.bai:md5,bf5167b68a29df979ea14a3cb148c4ac", - "Clone9_N3_mature_hairpin_genome.sorted.bam:md5,b80e7a38ab0f940047d39cd8ef3e1905", - "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,964b1ec118f45c5cb9443efc996b4b3e", - "Control_N1_mature_hairpin_genome.sorted.bam:md5,d153cfca67b7fd8fee388b22302c20c7", - "Control_N1_mature_hairpin_genome.sorted.idxstats:md5,6f43b2104f522103671ce78dc7d75b6d", - "Control_N1_mature_hairpin_genome.sorted.stats:md5,97f2c3ceb62b98d9169b226e954a1150", - "Control_N1_mature_hairpin_genome.sorted.bam.bai:md5,dc7706620275f5a43b52066970c1474d", - "Clone9_N3_mature_hairpin_genome.sorted.idxstats:md5,6561bdbc8589548d965823d7f43dee39", - "Clone1_N1_mature_hairpin_genome.sorted.idxstats:md5,f6408e25770f9a8530126900c314332f", - "Clone9_N3_mature_hairpin_genome.sorted.bam.bai:md5,5fa626110a289ede3549c4c73b53d714" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:39:09.615825899" - }, - "software_versions": { - "content": [ - "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, CAT_FASTQ={cat=8.3}, FASTP={fastp=0.23.4}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_GENOME={bowtie=1.3.1}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:39:09.345801293" - }, - "mirna_quant": { - "content": [ - "Control_N1_mature_hairpin.sorted.stats:md5,41ed031d9ee3d775fab782beea7c2c5e", - "Control_N1_mature_hairpin.sorted.idxstats:md5,2bb41d5a20116c7457ef45c1b294d22d", - "Clone9_N3_mature_hairpin.sorted.flagstat:md5,79f3d50c45d9aa0d2525f5f1411e8dd5", - "Control_N1_mature_hairpin.sorted.bam.bai:md5,b901e66cbdd91b38b32c49671c2b0538", - "Control_N1_mature_hairpin.sorted.flagstat:md5,e727c4751070cf76ebfd484c0e37d990", - "Control_N1_mature_hairpin.sorted.bam:md5,579a1e43d1a6205ac2c118c1b39bbdae", - "Clone1_N1_mature_hairpin.sorted.idxstats:md5,f2a16cf301d8cfd5f9f99edb610705c7", - "Clone9_N3_mature_hairpin.sorted.idxstats:md5,98db6ef38c05a65ee7ef5a7520f4f51c", - "Clone1_N1_mature_hairpin.sorted.bam.bai:md5,4bd9a2f4353cdc65a1db6edbdbab7a82", - "Clone1_N1_mature_hairpin.sorted.bam:md5,9557cc47f4e70261cc583b81fd3c55dd", - "Clone9_N3_mature_hairpin.sorted.stats:md5,52d607b29c6fae0a72cb55b83a5d550f", - "Clone1_N1_mature_hairpin.sorted.stats:md5,3fc6353abadc1c6e2687bc7a081f93a2", - "Clone9_N3_mature_hairpin.sorted.bam.bai:md5,75f78a876d94179713ce913a1dc43a79", - "Clone1_N1_mature_hairpin.sorted.flagstat:md5,f6d7848cf9c70cd3469ce1944d17be3c", - "Clone9_N3_mature_hairpin.sorted.bam:md5,d04faf5b2a33091861b1687e78ad23c7", - "Control_N1_mature.sorted.bam.bai:md5,01b52ea90bacac2ed44b4b165b03fe1f", - "Clone1_N1_mature.sorted.stats:md5,edfa6dab3271e66f743da2aca3ea7663", - "Clone9_N3_mature.sorted.bam:md5,d0fcf12036df675761eddb6e03eee657", - "Clone9_N3_mature.sorted.stats:md5,4fe47f64e7bdd0e1efeaa8271e92000a", - "Clone1_N1_mature.sorted.bam:md5,09f0d3c5b4e216d300904235fbb82494", - "Control_N1_mature.sorted.bam:md5,b2947881dd6b9631d701e175b7ac77e4", - "Control_N1_mature.sorted.stats:md5,9abec7b88211f78d0e743dbedb1e1125", - "Control_N1_mature.sorted.idxstats:md5,8e96945e95b03c3c33867c98dece1e4e", - "Clone9_N3_mature.sorted.idxstats:md5,f92b6bdb8bf206757d8e2733f60f3c1b", - "Clone9_N3_mature.sorted.flagstat:md5,bbb6bc880f6fc9424fc16b095af752b9", - "Clone9_N3_mature.sorted.bam.bai:md5,2504e62544b9f89fdbe2e8ad20b7e727", - "Clone1_N1_mature.sorted.bam.bai:md5,97c3b9ace9b0451ca7f6b9230e64bbfa", - "Clone1_N1_mature.sorted.idxstats:md5,f80f8349d8a814e8f67ef4c30e2f6a53", - "Clone1_N1_mature.sorted.flagstat:md5,e6adf8d4926033f9ae6a0d5ab42bd267", - "Control_N1_mature.sorted.flagstat:md5,f10e74138d682fed95c076112b7f9236", - "mirna.tsv:md5,b884a1dadb2a803fc3838f124695c68c", - "mirtop.tsv:md5,e82e7e158ad6541f7240d370c998b162", - "mirtop.gff:md5,e421a0dd1676ebdd331d4463fd7ec202", - "mirtop_rawData.tsv:md5,edae282cde52e6b60d42962479866cb3", - "mirtop_stats.txt:md5,3e59e311a62e873c7ec780d537d5e6a9", - "Control_N1.fastp_trimmed.fastq.gz:md5,8d0676323aa9e84556cdf209db92b6ed", - "Clone1_N1.fastp_trimmed.fastq.gz:md5,1ce9b5ab0591aa067c0bcfbc4852cd19", - "Clone9_N3.fastp_trimmed.fastq.gz:md5,abb626ba9f41ef35a3684d2b5b4f2c4f", - "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", - "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", - "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", - "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", - "mature_unmapped_read_counts.txt:md5,6f07c6c8054b843783c2b52888c12072", - "mature_normalized_CPM.txt:md5,025ac0731eb3817362983dcf6f3b4f79", - "hairpin_logtpm.csv:md5,4ac659c6e352ecd45970659eef009d33", - "mature_logtpm.txt:md5,9d0d4718cb7f72abbb26380745f42bc4", - "mature_edgeR_MDS_plot_coordinates.txt:md5,ef1fcf3b375b65c0611e32f1fa527759", - "hairpin_unmapped_read_counts.txt:md5,64a71970c8ebb5a7326f487c20685cee", - "mature_edgeR_MDS_distance_matrix.txt:md5,9b2553e2af74f3093386c88945d16514", - "mature_log2CPM_sample_distances.txt:md5,3e65534b731a92efdfe0373ff0b963ff", - "hairpin_log2CPM_sample_distances.txt:md5,2d89f929eff72230c1a6e8bffc8fa17a", - "hairpin_edgeR_MDS_distance_matrix.txt:md5,5001dc46960da9b83f7c528ad8116ddd", - "hairpin_logtpm.txt:md5,2bfc416b0011b131a5d2b8a4b8d3d7b5", - "hairpin_edgeR_MDS_plot_coordinates.txt:md5,f3ff4a57f6c4e8c9a3065c5fde85438b", - "mature_logtpm.csv:md5,2729c7b78855871f8b07804ab36ba8dd", - "hairpin_normalized_CPM.txt:md5,89c4abe13c09cd3e58b67a1e46e8e6e3", - "mature_counts.csv:md5,7714ee131dca993a1de82f22768db77d", - "hairpin_counts.csv:md5,55b0389a0a101bbf09a4718532f64514" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:39:11.127160605" - } -} \ No newline at end of file diff --git a/tests/test_umi.nf.test b/tests/test_umi.nf.test index 1901837d..b905c55c 100644 --- a/tests/test_umi.nf.test +++ b/tests/test_umi.nf.test @@ -18,171 +18,7 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 64 }, - - { assert snapshot( - path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.edited.fa"), - path("$outputDir/bowtie_index/genome/genome.3.ebwt"), - path("$outputDir/bowtie_index/genome/genome.4.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, - - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_contamination_check_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") - ).match("multiqc") }, - - { assert snapshot( - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam.bai"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats") - ).match("genome_quant") }, - - { assert snapshot( - path("$outputDir/umi_dedup/bam_deduplicated/SRX8195117_SRR11631013.umi_dedup.sorted.fastq.gz"), - path("$outputDir/umi_dedup/bam_deduplicated/SRX8195118_SRR11631014.umi_dedup.sorted.fastq.gz"), - path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195118_SRR11631014.umi_extract.fastq.gz"), - path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195117_SRR11631013.umi_extract.fastq.gz") - ).match("umi_dedup") }, - - { assert snapshot( - path("$outputDir/mirna_quant/bam/seqcluster/SRX8195117_SRR11631013_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/SRX8195118_SRR11631014_seqcluster.bam"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195117_SRR11631013_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195118_SRR11631014_seqcluster_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.bam"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/SRX8195118_SRR11631014_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/SRX8195117_SRR11631013_mature_hairpin_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam.bai"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.bam"), - path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195118_SRR11631014_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195117_SRR11631013_mature_unmapped.fq.gz"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.gff"), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt"), - path("$outputDir/mirna_quant/seqcluster/final/SRX8195117_SRR11631013.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/SRX8195118_SRR11631014.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt"), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt"), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv"), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv") - ).match("mirna_quant") }, - - { assert snapshot( - path("$outputDir/fastqc/raw/SRX8195117_SRR11631013.raw_fastqc.zip"), - path("$outputDir/fastqc/raw/SRX8195118_SRR11631014.raw_fastqc.zip"), - path("$outputDir/fastqc/trimmed/SRX8195117_SRR11631013.trim_fastqc.zip"), - path("$outputDir/fastqc/trimmed/SRX8195118_SRR11631014.trim_fastqc.zip") - ).match("fastqc") }, - - { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/SRX8195118_SRR11631014.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/SRX8195117_SRR11631013.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/SRX8195118_SRR11631014.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/SRX8195117_SRR11631013.fastp.fasta") - ).match("mirtrace") }, - + { assert workflow.trace.succeeded().size() == 64 } ) } diff --git a/tests/test_umi.nf.test.snap b/tests/test_umi.nf.test.snap deleted file mode 100644 index 2becd637..00000000 --- a/tests/test_umi.nf.test.snap +++ /dev/null @@ -1,217 +0,0 @@ -{ - "bowtie_index": { - "content": [ - "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", - "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", - "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", - "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", - "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", - "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", - "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", - "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", - "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", - "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", - "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", - "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", - "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", - "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", - "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", - "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", - "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", - "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", - "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:19.829287378" - }, - "mirtrace": { - "content": [ - "mirtrace-stats-rnatype.tsv:md5,00e584439bec82f5de8d6485a73dec37", - "mirtrace-stats-length.tsv:md5,3edbc31452dba97f8b829e3f8f635955", - "mirtrace-stats-contamination_detailed.tsv:md5,428d2fd6ea0a6f2af1018a557e89bece", - "mirtrace-stats-qcstatus.tsv:md5,de4f8a670b736bedf348d358cfdfb9fc", - "mirtrace-stats-contamination_basic.tsv:md5,3d54b37ab3206e9fec909fe3ea1a4777", - "mirtrace-stats-phred.tsv:md5,8cf9fc2223b9aeb50f92c8845edbf535", - "mirtrace-stats-mirna-complexity.tsv:md5,cd2f37963adeee159764a89688a4a6a5", - "SRX8195118_SRR11631014.fastp.fasta:md5,99e2ce92ce102bd3fedc3a9d3b926873", - "SRX8195117_SRR11631013.fastp.fasta:md5,e0e31d882568a7853dea75b3c595108f", - "SRX8195118_SRR11631014.fastp.fasta:md5,7db07b8c0b9e2b484eb3d42a04e480d1", - "SRX8195117_SRR11631013.fastp.fasta:md5,eb1ba9fa6f7d956e5d650fdd306d5634" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:46.029580614" - }, - "umi_dedup": { - "content": [ - "SRX8195117_SRR11631013.umi_dedup.sorted.fastq.gz:md5,247d78a2d700012064d0b2e28d04b061", - "SRX8195118_SRR11631014.umi_dedup.sorted.fastq.gz:md5,af2b98d9bd6d0760a7eb07813d015aee", - "SRX8195118_SRR11631014.umi_extract.fastq.gz:md5,d2928324ae465d3d8eaf65c24418b8cf", - "SRX8195117_SRR11631013.umi_extract.fastq.gz:md5,1aeed318fab39fa646ff790a025bd21d" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:20.579451915" - }, - "genome_quant": { - "content": [ - "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam.bai:md5,a2550ac81a655836969f91a4fbf64cf6", - "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats:md5,a4874de294706a7ead30258944ff2dad", - "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam:md5,b0534300df725919db7e38a8215d22b4", - "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam:md5,2dbac90f7439b878605b920ea7aa66a9", - "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats:md5,cc0413bf90252c3b3af8926fd64bc873", - "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat:md5,977e88cbe62027285df73e1f7f9cd9bc", - "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.flagstat:md5,235383f64a943885f5d899f5b8e03eba", - "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam.bai:md5,51444acc5b1c67d4bba3809a40e1ffd3", - "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats:md5,053912820064080299710bfbe7baf3c7", - "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats:md5,e19093f62044a7d053a0073092c506f3" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:20.293351627" - }, - "software_versions": { - "content": [ - "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTP_LENGTH_FILTER={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_GENOME={bowtie=1.3.1}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, UMICOLLAPSE_FASTQ={umicollapse=1.0.0-1}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:19.827254847" - }, - "fastqc": { - "content": [ - "SRX8195117_SRR11631013.raw_fastqc.zip:md5,26a041b01b10149a90a1a9233cb5cfd8", - "SRX8195118_SRR11631014.raw_fastqc.zip:md5,8a4b0ed8cf615100055caf5eb66afc9f", - "SRX8195117_SRR11631013.trim_fastqc.zip:md5,626143589a7acc028b2ecd01f687f03f", - "SRX8195118_SRR11631014.trim_fastqc.zip:md5,26ab263d79de53ded2eeb0d3a905f82e" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:36.864495018" - }, - "multiqc": { - "content": [ - "fastqc-status-check-heatmap.txt:md5,c1509fdd74b21a718fe099de64514995", - "fastp_filtered_reads_plot.txt:md5,3aaa79e1ede44347971c26100d9e954b", - "fastqc_top_overrepresented_sequences_table-1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "fastqc_sequence_counts_plot-1.txt:md5,24744e039ce4dbcbacf42edbfd642a8b", - "mirtrace_complexity_plot.txt:md5,5a860a872f793250b8c4482d031176a8", - "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,351f949c0abf4fb7587f3f5d9a28d461", - "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", - "samtools-stats-dp.txt:md5,74808822577fb62efb39811272e6919e", - "fastqc_sequence_length_distribution_plot.txt:md5,8c34b57ec084e2da9d62c254c0a517f4", - "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,dfdb23f41359b8a6b84d6626a0474d02", - "fastqc_sequence_duplication_levels_plot-1.txt:md5,b5ae95ecd73055798ed70947dda3747c", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,89adfa92b1cde0ad4e401b430bbc68ce", - "multiqc_general_stats.txt:md5,b56535ef53b3ca4477aac99845712fa5", - "fastqc_per_base_n_content_plot-1.txt:md5,db081d3aa63007e5a78113f0fc26f27d", - "fastqc_per_base_n_content_plot.txt:md5,5b5b8cee3162d092c0bcddffbd000f34", - "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,66a47c7ce00ede2053f8e6eb20ec3417", - "fastqc_per_sequence_quality_scores_plot.txt:md5,3aa99649540afc898d32d2e49a364487", - "mirtrace_qc_plot.txt:md5,b08d11ea51c54e615f9608002644c787", - "fastqc_per_sequence_quality_scores_plot-1.txt:md5,4108da6fe352558a652ee2b17d609e07", - "mirtrace_length_plot.txt:md5,440a84ce9bbdb89b736e4e2446382665", - "fastqc_top_overrepresented_sequences_table.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "fastqc-status-check-heatmap-1.txt:md5,cb2ea844834808ae4c95c6440269cf2e", - "fastqc_sequence_counts_plot.txt:md5,5e5c5132ff1969dfa40cb8b1eadf7a46", - "mirtrace_rna_categories_plot.txt:md5,6d08c297377a6241c4c1e82278d71f32", - "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,f36b7cfd3057b26281367397db45033a", - "samtools_alignment_plot.txt:md5,5e828961dbd55a6d6872221c49dfdc59", - "fastqc_per_base_sequence_quality_plot.txt:md5,e2e187bc0b0c1f0d1abb3b666945c7b3", - "mirtop_read_count_plot.txt:md5,2603cd59d95e71863e264ca9589591fa", - "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,bbad2035ada86867c4ed579a93b78d64", - "mirtop_unique_read_count_plot.txt:md5,5082d66ba230c780e87b78be589a2c3d", - "mirtop_mean_read_count_plot.txt:md5,5e2897fd0291f6e81a350786620f9b5a", - "mirtrace_contamination_check_plot.txt:md5,7f12917ce506127a729edb733fdda511", - "fastqc_adapter_content_plot.txt:md5,de1d7324ff5146b49fc9a2e6d4633962", - "fastqc_sequence_duplication_levels_plot.txt:md5,fe7598e49f93bb980a7675a2bb4bd3b5", - "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,c2f2f9282a50c3eef475664cc969b8ec", - "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,15d8fa32e0c11ef0d3d10fc28370972c", - "fastqc_adapter_content_plot-1.txt:md5,89cd342fdc6fbba5f67078c9a2f0c684", - "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,f832e92fb36db181ed1079be110edb2a", - "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,488e25de89d18d20f29b86f2580a8df9", - "multiqc_sources.txt:md5,e3350035ab949e3f5093d506077b0fe0", - "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,d673e3b18c40c5af1edccffba386d678" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:20.057500216" - }, - "mirna_quant": { - "content": [ - "SRX8195117_SRR11631013_seqcluster.bam:md5,822cab8f3a85ddb27697cff48c702a2e", - "SRX8195118_SRR11631014_seqcluster.bam:md5,909d3ed731707db889ef6a2d1ca85aba", - "SRX8195117_SRR11631013_seqcluster_unmapped.fq.gz:md5,203db6b7864395ef7404e79d070a3ef4", - "SRX8195118_SRR11631014_seqcluster_unmapped.fq.gz:md5,c231087a920084e50ea28295e0af8797", - "SRX8195117_SRR11631013_mature_hairpin.sorted.idxstats:md5,4e7c1c98804febf6210cee5e3941709e", - "SRX8195118_SRR11631014_mature_hairpin.sorted.flagstat:md5,e0c44533bc7813d552de4864d997c916", - "SRX8195118_SRR11631014_mature_hairpin.sorted.idxstats:md5,f4485713620f31d97a5006acdf6d8a5d", - "SRX8195117_SRR11631013_mature_hairpin.sorted.stats:md5,b3ff5680bfebaaf6e30bb43a29a3031c", - "SRX8195117_SRR11631013_mature_hairpin.sorted.flagstat:md5,b86bd14dc687a26ba5a84d1015f4b70a", - "SRX8195118_SRR11631014_mature_hairpin.sorted.bam.bai:md5,5fb71506c8851af43d409ecd9fb1a13f", - "SRX8195118_SRR11631014_mature_hairpin.sorted.bam:md5,029b8b419ab9f61f6a45c00402ae4aa7", - "SRX8195117_SRR11631013_mature_hairpin.sorted.bam.bai:md5,82678a34d83ae306d0c6330c6b03b05a", - "SRX8195117_SRR11631013_mature_hairpin.sorted.bam:md5,4e047885963edc0e8848c68dcaaf28ec", - "SRX8195118_SRR11631014_mature_hairpin.bam:md5,4086b11369207f2ef469e52b59799d59", - "SRX8195118_SRR11631014_mature_hairpin.sorted.stats:md5,da76c29d304c53210242909c3e23a29a", - "SRX8195117_SRR11631013_mature_hairpin.bam:md5,ca5e172d1cb9dad640523a3fcf30cb7c", - "SRX8195118_SRR11631014_mature_hairpin_unmapped.fq.gz:md5,1a2c340984aa2e571b9cc2e7f4823356", - "SRX8195117_SRR11631013_mature_hairpin_unmapped.fq.gz:md5,b4402f45bb1984ed5f919d802df28fbd", - "SRX8195117_SRR11631013_mature.sorted.bam.bai:md5,d62ec895b633eea65fe783249aa4aaa7", - "SRX8195118_SRR11631014_mature.sorted.idxstats:md5,8b9cf0f1647b938f058b80522df24667", - "SRX8195117_SRR11631013_mature.sorted.bam:md5,5e20be9c8d3201b5ffa6eadbad06b699", - "SRX8195118_SRR11631014_mature.bam:md5,3ef1863216a59735fc12a258c847bebc", - "SRX8195117_SRR11631013_mature.sorted.flagstat:md5,171387fb18ba9868e28ca03d24a7daca", - "SRX8195118_SRR11631014_mature.sorted.stats:md5,bf67cbae75e68e5de07d042487010498", - "SRX8195118_SRR11631014_mature.sorted.flagstat:md5,57c6d477394d367ebae59f7267b430a5", - "SRX8195117_SRR11631013_mature.sorted.stats:md5,c5ed9f69f29172af201968f97b49be67", - "SRX8195118_SRR11631014_mature.sorted.bam:md5,d55bec2368640fede5da1704dbccfb94", - "SRX8195117_SRR11631013_mature.sorted.idxstats:md5,fb6c4000f82a66654b4f2a40570649b5", - "SRX8195118_SRR11631014_mature.sorted.bam.bai:md5,882a03bf714b0ba388496ef3b8df76e7", - "SRX8195117_SRR11631013_mature.bam:md5,125a84bae34979111a25f26e30c2a07e", - "SRX8195118_SRR11631014_mature_unmapped.fq.gz:md5,4d20ecfb8963b9ff1b03825dd3c4c365", - "SRX8195117_SRR11631013_mature_unmapped.fq.gz:md5,dab237af96d3d48d48168337e1aa117d", - "mirna.tsv:md5,e30f3037522a0a20f2a4b32cbb70990a", - "mirtop.tsv:md5,6c83e7efc40b4dc94d63259aa57b22c8", - "mirtop.gff:md5,29d876ccb32a8ed95da4ae8b6b1c08a7", - "mirtop_rawData.tsv:md5,ed4a0ceb2e8cd1721aa5ed27270f9623", - "mirtop_stats.txt:md5,9dcdf713a5096c123e32f7c2823c4451", - "SRX8195117_SRR11631013.fastp_trimmed.fastq.gz:md5,0a0da4dc5c49678d8421537dbf3067bc", - "SRX8195118_SRR11631014.fastp_trimmed.fastq.gz:md5,cf4de7d3978d5ff4709a88d3d2d034d8", - "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", - "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", - "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", - "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", - "mature_unmapped_read_counts.txt:md5,d2bc7fbe481ea26a72d7a5f35343fa8b", - "mature_normalized_CPM.txt:md5,57aa77072446dbaf32cbada7b085ee09", - "hairpin_logtpm.csv:md5,1435ade38403ded966117ba52bbbbaec", - "mature_logtpm.txt:md5,950dc03ce0c2e4e28fc6512aa307dcc2", - "hairpin_unmapped_read_counts.txt:md5,b6bf9d21c775ce6c9ef48a3d4ecf4d6b", - "hairpin_logtpm.txt:md5,0abfd7800b04a2b8fbe5ac8b683d6ca1", - "mature_logtpm.csv:md5,081545598a64d691050ebc0e52e783c0", - "hairpin_normalized_CPM.txt:md5,6176bf533f063247be51a02049e80add", - "mature_counts.csv:md5,dd82aef87b563b63c62cbab5a177025c", - "hairpin_counts.csv:md5,a7129322910eae9291d10820403a3491" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-19T21:49:27.68981406" - } -} \ No newline at end of file From 38521e9c68bc7ca548212e1fec40391ba965b029 Mon Sep 17 00:00:00 2001 From: zxBIB Schcolnicov Date: Wed, 21 Aug 2024 23:31:49 +0200 Subject: [PATCH 05/15] Standardized changelog and generated nf-tests --- CHANGELOG.md | 15 +- tests/test.nf.test | 274 ++++++++++++++++++- tests/test.nf.test.snap | 319 ++++++++++++++++++++++ tests/test_index.nf.test | 241 +++++++++++++++- tests/test_index.nf.test.snap | 292 ++++++++++++++++++++ tests/test_mirgenedb.nf.test | 237 +++++++++++++++- tests/test_mirgenedb.nf.test.snap | 275 +++++++++++++++++++ tests/test_no_genome.nf.test | 272 +++++++++++++++++- tests/test_no_genome.nf.test.snap | 311 +++++++++++++++++++++ tests/test_technical_repeats.nf.test | 120 +++++++- tests/test_technical_repeats.nf.test.snap | 153 +++++++++++ tests/test_umi.nf.test | 166 ++++++++++- tests/test_umi.nf.test.snap | 217 +++++++++++++++ 13 files changed, 2879 insertions(+), 13 deletions(-) create mode 100644 tests/test.nf.test.snap create mode 100644 tests/test_index.nf.test.snap create mode 100644 tests/test_mirgenedb.nf.test.snap create mode 100644 tests/test_no_genome.nf.test.snap create mode 100644 tests/test_technical_repeats.nf.test.snap create mode 100644 tests/test_umi.nf.test.snap diff --git a/CHANGELOG.md b/CHANGELOG.md index 8c27546e..d113644e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,16 +5,17 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ## v2.4.0dev - 2024-XX-XX - X -- [[#332]](https://github.com/nf-core/smrnaseq/issues/332) by [[#361]](https://github.com/nf-core/smrnaseq/pull/361) - Fix documentation to use only single-end - [[#349]](https://github.com/nf-core/smrnaseq/pull/349) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347), change conda-base to conda-forge channel -- [[#350]](https://github.com/nf-core/smrnaseq/pull/350) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347), set python version to 3.7 to fix pysam issue -- [[#351]](https://github.com/nf-core/smrnaseq/issues/351) - Fix [Protocol inheritance issue](https://github.com/nf-core/smrnaseq/pull/364) - fixing protocol inheritance from subworkflow with move to config profile(s) for different protocols. -- [[#369]](https://github.com/nf-core/smrnaseq/issues/369) - Fix [Linting](https://github.com/nf-core/smrnaseq/pull/377) - Fixed linting warnings and updated modules & subworkflows. +- [[#350]](https://github.com/nf-core/smrnaseq/pull/350) - Fix [MIRTOP_QUANT conda issue](https://github.com/nf-core/smrnaseq/issues/347), set python version to 3.7 to fix pysam issue. +- [[#361]](https://github.com/nf-core/smrnaseq/pull/361) by [[#332]](https://github.com/nf-core/smrnaseq/issues/332) - Fix documentation to use only single-end. +- [[#364]](https://github.com/nf-core/smrnaseq/pull/364) - Fix [Protocol inheritance issue](https://github.com/nf-core/smrnaseq/issues/351) - fixing protocol inheritance from subworkflow with move to config profile(s) for different protocols. +- [[#372]](https://github.com/nf-core/smrnaseq/pull/372) - Fix [Plain test profile](https://github.com/nf-core/smrnaseq/issues/371) - Updated default protocol value to "custom". - [[#374]](https://github.com/nf-core/smrnaseq/pull/374) - Fix [default tests](https://github.com/nf-core/smrnaseq/issues/375) so that they do not require additional profiles in CI. Change GitHub CI fail-fast strategy to false. -- [[#371]](https://github.com/nf-core/smrnaseq/issues/371) - Fix [Plain test profile](https://github.com/nf-core/smrnaseq/pull/372) - Updated default protocol value to "custom". -- [[#380]](https://github.com/nf-core/smrnaseq/pull/380) - Fix checking number of samples which causes error in plotMDS. Add nf-tests for local modules using custom R scripts: [edgeR_mirBase.R](https://github.com/nf-core/smrnaseq/issues/187). -- [[#378]](https://github.com/nf-core/smrnaseq/pull/378) - Fix [`--mirtrace_species` bug](<(https://github.com/nf-core/smrnaseq/issues/348)>). Make `MIRTRACE` process conditional. Add mirgenedb test. - [[#375]](https://github.com/nf-core/smrnaseq/pull/375) - Test merging of [technical repeats](https://github.com/nf-core/smrnaseq/issues/212). +- [[#377]](https://github.com/nf-core/smrnaseq/pull/377) - Fix [Linting](https://github.com/nf-core/smrnaseq/issues/369) - Fixed linting warnings and updated modules & subworkflows. +- [[#378]](https://github.com/nf-core/smrnaseq/pull/378) - Fix [`--mirtrace_species` bug](<(https://github.com/nf-core/smrnaseq/issues/348)>). Make `MIRTRACE` process conditional. Add mirgenedb test. +- [[#380]](https://github.com/nf-core/smrnaseq/pull/380) - Fix checking number of samples which causes error in plotMDS. Add nf-tests for local modules using custom R scripts: [edgeR_mirBase.R](https://github.com/nf-core/smrnaseq/issues/187). +- [[#381]](https://github.com/nf-core/smrnaseq/pull/381) - Update CI tests to nf-tests [Convert tests to nf-tests](https://github.com/nf-core/smrnaseq/issues/379). - [[#382]](https://github.com/nf-core/smrnaseq/pull/382) - Add nf-tests for local modules using custom R scripts: [collapse_mirtop.R](https://github.com/nf-core/smrnaseq/issues/174). ## v2.3.1 - 2024-04-18 - Gray Zinc Dalmation Patch diff --git a/tests/test.nf.test b/tests/test.nf.test index 3d766b2b..e161bbfa 100644 --- a/tests/test.nf.test +++ b/tests/test.nf.test @@ -18,7 +18,279 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 196 } + { assert workflow.trace.succeeded().size() == 196 }, + + { assert snapshot( + path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.edited.fa"), + path("$outputDir/bowtie_index/genome/genome.3.ebwt"), + path("$outputDir/bowtie_index/genome/genome.4.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") + ).match("bowtie_index") }, + + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), + path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") + ).match("multiqc") }, + + { assert snapshot( + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai").exists() + ).match("genome_quant") }, + + { assert snapshot( + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop.tsv").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop.gff").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists(), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists() + ).match("mirna_quant") }, + + { assert snapshot( + path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip").exists() + ).match("fastqc") }, + + { assert snapshot( + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") + ).match("mirtrace") }, + ) } diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap new file mode 100644 index 00000000..d7f9fc23 --- /dev/null +++ b/tests/test.nf.test.snap @@ -0,0 +1,319 @@ +{ + "bowtie_index": { + "content": [ + "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", + "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", + "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", + "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", + "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", + "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", + "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", + "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", + "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", + "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", + "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", + "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", + "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", + "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", + "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", + "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", + "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", + "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", + "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-20T19:07:54.749575939" + }, + "mirtrace": { + "content": [ + "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", + "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", + "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", + "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", + "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", + "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", + "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638", + "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", + "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", + "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", + "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", + "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", + "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", + "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", + "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8", + "Clone1_N1.fastp.fasta:md5,e297dfa46353946d6c140e4513dd4525", + "Clone9_N1.fastp.fasta:md5,63a17d136548fc98f34c8d98006cc7da", + "Control_N3.fastp.fasta:md5,d9980a598ece252e19d6c9ebefd51861", + "Control_N1.fastp.fasta:md5,e964e05ce2c93937a8e76602f2e08150", + "Clone9_N2.fastp.fasta:md5,b1ca39e6e1e75ee7d654d9ccfb35e906", + "Control_N2.fastp.fasta:md5,8cefbc494be7b363b19c10b8c00366b2", + "Clone1_N3.fastp.fasta:md5,4012282462dde0750f09cec883304cc3", + "Clone9_N3.fastp.fasta:md5,f733e20eb8d2a2009ca82464e8ccb148" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-20T19:08:08.930618317" + }, + "genome_quant": { + "content": [ + "Clone9_N2_mature_hairpin_genome.sorted.flagstat:md5,b8fbbdaca0458b19732312dea2997be8", + "Control_N1_mature_hairpin_genome.sorted.flagstat:md5,18f0028f1cfc137ef8f089e465fe20f5", + "Control_N2_mature_hairpin_genome.sorted.flagstat:md5,b0d42e94b2e0e026cd32a88dce40722c", + "Control_N3_mature_hairpin_genome.sorted.stats:md5,53e8fca566dd5dd8553b25c38e961f6b", + "Clone1_N3_mature_hairpin_genome.sorted.stats:md5,fb089da3351a3f8c0bc742f3f4533349", + "Clone9_N3_mature_hairpin_genome.sorted.stats:md5,8ec73033ee0e2ad16fdc497b209adb50", + "Clone9_N3_mature_hairpin_genome.sorted.flagstat:md5,dbe38679a68d55b8a182831e336eebb1", + true, + "Clone1_N1_mature_hairpin_genome.sorted.flagstat:md5,4d552770e6d3b06775b6f484684f7a77", + "Control_N2_mature_hairpin_genome.sorted.stats:md5,f105861208044e44644c74449d0c6142", + "Control_N2_mature_hairpin_genome.sorted.idxstats:md5,b6da32ce230fdeab39f3c4d5dcf41a3a", + true, + true, + true, + "Clone1_N3_mature_hairpin_genome.sorted.idxstats:md5,d680e48370d319f1891cdd61b8754644", + true, + "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,64b19984a4c2fa55e69a28fe7c138d7c", + true, + true, + true, + "Control_N3_mature_hairpin_genome.sorted.flagstat:md5,ae834e3dbaa18aa9bce66c3b0034c430", + "Clone9_N1_mature_hairpin_genome.sorted.idxstats:md5,a199f8999ba915a81acfc450e0db8393", + true, + "Control_N1_mature_hairpin_genome.sorted.idxstats:md5,fe01b41ed88612c28b667817c4a8fcc1", + true, + true, + "Clone1_N3_mature_hairpin_genome.sorted.flagstat:md5,9dee041c82ad3b2d2ab4f8986822f2ce", + true, + "Control_N1_mature_hairpin_genome.sorted.stats:md5,b2afcfcb9e785a71bb5fce25b87fd67a", + true, + "Control_N3_mature_hairpin_genome.sorted.idxstats:md5,94d53c9ad335779a1ea25fd5b4b08069", + true, + "Clone9_N2_mature_hairpin_genome.sorted.stats:md5,6db5d451fa95a77247d38c4a263cf05d", + "Clone9_N1_mature_hairpin_genome.sorted.stats:md5,f819db926f570a9bb1cf9b6adff7d758", + "Clone9_N3_mature_hairpin_genome.sorted.idxstats:md5,0a227abfa6aa10023219bce7b2795b67", + "Clone9_N1_mature_hairpin_genome.sorted.flagstat:md5,2fd8cd41edde2292f857528658c3e0a1", + "Clone9_N2_mature_hairpin_genome.sorted.idxstats:md5,61c4821cba66c91272e62547617db2c9", + true, + "Clone1_N1_mature_hairpin_genome.sorted.idxstats:md5,169a196ee2da6945392f6a361164ffc5", + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-20T19:07:57.99297214" + }, + "software_versions": { + "content": [ + "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_GENOME={bowtie=1.3.1}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-20T19:07:54.725875671" + }, + "fastqc": { + "content": [ + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-20T19:08:04.091935019" + }, + "multiqc": { + "content": [ + "fastqc-status-check-heatmap.txt:md5,30f55902420433a11971d36956e8576e", + "fastp_filtered_reads_plot.txt:md5,0af4d3cfbf463f33b2b88cdfd69909ac", + "fastqc_overrepresented_sequences_plot.txt:md5,d861a4a956a3023efa19b1259d8665b2", + true, + "fastqc_sequence_counts_plot-1.txt:md5,37d8ae6c5734eb2679e65e46c9af9101", + "mirtrace_complexity_plot.txt:md5,5f78d6f559a9642e68e1fd74ac2c11ca", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", + "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", + "samtools-stats-dp.txt:md5,61a77aab820a3eba21a51e32168b45e3", + "fastqc_sequence_length_distribution_plot.txt:md5,13f72b3be854c74cd7b5176ca0583770", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "fastqc_sequence_duplication_levels_plot-1.txt:md5,06a4162d4787883b1f39a1b9acb7bb91", + "fastqc_per_base_sequence_quality_plot-1.txt:md5,6a0df664a369ee216412f0033ed3a042", + true, + "fastqc_per_base_n_content_plot-1.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "fastqc_per_base_n_content_plot.txt:md5,fb8a49467d1679dbf716e1f00c1f25e5", + "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,b1481a9fbf5ea541b39aed99b51d616f", + "fastqc_per_sequence_quality_scores_plot.txt:md5,38dbd6509de7f1beac17e44acb8336be", + "mirtrace_qc_plot.txt:md5,c436d017382baed6617fc3c1ad8ab41d", + "fastqc_per_sequence_quality_scores_plot-1.txt:md5,69f4459318311103fe71a5d1d3b2c076", + "mirtrace_length_plot.txt:md5,2366f10eb8bd3c32d2b35e2df20c786c", + true, + "fastqc_overrepresented_sequences_plot-1.txt:md5,1de000de50cc7516bb9d996def14c6eb", + "fastqc-status-check-heatmap-1.txt:md5,e64c353797e6dc057d10b3194ca6b20d", + "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", + "mirtrace_rna_categories_plot.txt:md5,8665376e2a123e1661f82cbbee54789f", + "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", + "samtools_alignment_plot.txt:md5,f87f3d2101f70e840c57df850bd1e3be", + "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", + true, + "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + true, + true, + "fastqc_adapter_content_plot.txt:md5,86a0f478fd3e690ef5132d08bf4e7625", + "fastqc_sequence_duplication_levels_plot.txt:md5,88b0babe77f623547e8af664791ef2d0", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,539883757ae5bf731da93fe0568022e9", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,ed7205b9c46d5f431c5b3bf499a673a1", + "fastqc_adapter_content_plot-1.txt:md5,71ba0983a71f3a833526ab83a985d072", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,a8387a3e6b350acd16bb0ed5a43949d8", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3e9c1a7204c12d9c1b3b53342cf61840", + true, + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,efa8123c9ad43f99a6fba671f50322ca" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-20T19:07:57.481787644" + }, + "mirna_quant": { + "content": [ + "Control_N1_mature_hairpin.sorted.stats:md5,feb69ad2f8bbc527e39502a297f08abd", + "Control_N1_mature_hairpin.sorted.idxstats:md5,e1f455195f1cb42a1d1e58770aaeb2b4", + "Clone1_N3_mature_hairpin.sorted.flagstat:md5,6f14ec4cd502c0eb213b1905b4568a76", + "Clone9_N2_mature_hairpin.sorted.stats:md5,7bb8654d44dac245aec6aa045250628a", + "Clone9_N3_mature_hairpin.sorted.flagstat:md5,efc65cb620ca139b19967e12f13ba007", + true, + true, + "Control_N1_mature_hairpin.sorted.flagstat:md5,41769a400a176ea78432749f07f80fda", + true, + "Clone9_N1_mature_hairpin.sorted.stats:md5,155f327a9be0afa9584ec426826b5457", + true, + "Control_N2_mature_hairpin.sorted.stats:md5,1195dd51f77e338db83dc66476ac7c5f", + true, + "Control_N3_mature_hairpin.sorted.idxstats:md5,2c44710ce63bdebb12d64c729ef338b0", + true, + true, + "Clone1_N1_mature_hairpin.sorted.idxstats:md5,0bca2d01f734128f3c11cf2697433048", + "Clone9_N3_mature_hairpin.sorted.idxstats:md5,9523d29d411c2efb0a1756355230fa98", + "Control_N2_mature_hairpin.sorted.idxstats:md5,8859b6e432cef8b24d5fb258a06aaabe", + "Clone9_N2_mature_hairpin.sorted.flagstat:md5,663ae0bb8b29d1e1c3d75ef5df1015a4", + "Clone9_N1_mature_hairpin.sorted.flagstat:md5,3e4b295b54df05c438603edaa53123b1", + "Control_N3_mature_hairpin.sorted.flagstat:md5,f3df866b94dc6ef355b01f22047aaf4f", + true, + true, + true, + "Clone9_N3_mature_hairpin.sorted.stats:md5,9f61c028bb1c92667e31093156ada662", + "Clone1_N1_mature_hairpin.sorted.stats:md5,bd02cb15e666054edecc89d392d72902", + "Clone9_N2_mature_hairpin.sorted.idxstats:md5,04b1c0ea4f133b5ee9086eec1f4077e7", + "Clone1_N3_mature_hairpin.sorted.stats:md5,471db325d8ccd1fe787b5dd91dccf487", + true, + "Control_N2_mature_hairpin.sorted.flagstat:md5,2605548b5ab1e6ad6b5cf88ea0030909", + "Clone9_N1_mature_hairpin.sorted.idxstats:md5,238b462a2418d545418c0b3a28029bdf", + true, + "Control_N3_mature_hairpin.sorted.stats:md5,2f2249c537451d1f72dfe298f16093ac", + true, + true, + "Clone1_N1_mature_hairpin.sorted.flagstat:md5,8d0c785fec7b300200863c68b158444c", + true, + true, + "Clone1_N3_mature_hairpin.sorted.idxstats:md5,5b6cd8d5784c387d2649f18499a17c6e", + true, + "Clone1_N1_mature.sorted.stats:md5,9c42ffda181ca24ab076efc16fcfd4b3", + "Clone1_N3_mature.sorted.idxstats:md5,805f115ac4d9c8033908bafaba6c92fb", + "Clone9_N2_mature.sorted.stats:md5,fb8c403012481dafb895013c555f6d85", + "Control_N2_mature.sorted.stats:md5,ef5935898e3ca45d898053af335d1dfb", + "Control_N3_mature.sorted.flagstat:md5,2831f55bccbcf666d1c313ef377bcb30", + true, + true, + "Clone9_N3_mature.sorted.stats:md5,23b012dd60ea6dcec5cedb5a73ffc792", + true, + "Clone1_N3_mature.sorted.flagstat:md5,67fc6ba8516d4e5b3ed2a62febc92f0a", + "Clone9_N1_mature.sorted.idxstats:md5,c6eb22f3ff675e422d065375279150b2", + true, + "Control_N1_mature.sorted.stats:md5,b4ffb3a7623e32420def4d3470a326ab", + "Control_N1_mature.sorted.idxstats:md5,847bc5c6ef44e1f9754e47e648a5ef98", + "Clone9_N2_mature.sorted.flagstat:md5,247e02da50509fc1b3c5b35001922a8d", + "Control_N2_mature.sorted.flagstat:md5,c8742d1b49535ff815c2def66cba681e", + true, + true, + true, + "Control_N2_mature.sorted.idxstats:md5,12388de965d69b6102b62bc9cdf27e85", + true, + "Clone9_N1_mature.sorted.flagstat:md5,014b846757652783ff3f954a966b8a1b", + true, + true, + "Clone9_N3_mature.sorted.idxstats:md5,dee54e8e22dfca24acc290bf89a05cd4", + "Clone9_N2_mature.sorted.idxstats:md5,c9643d610de2f4d449a876e41dcab872", + "Clone9_N3_mature.sorted.flagstat:md5,4f60cfd3527e91df204253f9f1aebfcd", + "Control_N3_mature.sorted.idxstats:md5,5fb7b46915043bd3c947a37afc3e8075", + true, + true, + "Clone1_N1_mature.sorted.idxstats:md5,77ed64ddd23cf07340b65c04559d4726", + true, + "Clone1_N1_mature.sorted.flagstat:md5,f138a532bc7dab94f7cf4b4a4e5e23e5", + "Control_N3_mature.sorted.stats:md5,ff9dab4d3220aa44cdc80ea2fc311823", + "Clone1_N3_mature.sorted.stats:md5,e8feced949af44c8e5d31523b12122b9", + true, + true, + "Control_N1_mature.sorted.flagstat:md5,16318a574fe410b81c0e2cdf0dfa3c97", + "Clone9_N1_mature.sorted.stats:md5,02184884c17c8730f4df9e1a6144bbdc", + "mirna.tsv:md5,1f840afe7ab68eac73feaaad321b64f6", + true, + true, + "mirtop_rawData.tsv:md5,774410dd2cf1e5be83bf8d6e1e8b96b0", + true, + "Clone1_N3.fastp_trimmed.fastq.gz:md5,2e395240c74b3870efe03dc329d8bad8", + "Control_N1.fastp_trimmed.fastq.gz:md5,2f09082eb68a8f1dc308050e330887ec", + "Control_N3.fastp_trimmed.fastq.gz:md5,342368a6e6acdaf0ae9379676b6d07f0", + "Clone9_N1.fastp_trimmed.fastq.gz:md5,115cf0c346a93a47ba782c5724b4f090", + "Clone1_N1.fastp_trimmed.fastq.gz:md5,14a2590e663dbde105780726c2173c25", + "Clone9_N2.fastp_trimmed.fastq.gz:md5,c922ec95a4b84d806dd2054ff0f9cab7", + "Clone9_N3.fastp_trimmed.fastq.gz:md5,67cf9a7d2fa431f0e772391ed1651f93", + "Control_N2.fastp_trimmed.fastq.gz:md5,d6e607edcb3d71c546ce8fdfb18e3999", + "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", + "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", + "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + true, + true, + true, + true, + true, + true, + true, + true, + "hairpin_log2CPM_sample_distances.txt:md5,b19fa1d9f821fc8e2c0e9f34f76b5479", + true, + true, + true, + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T17:33:19.815567664" + } +} \ No newline at end of file diff --git a/tests/test_index.nf.test b/tests/test_index.nf.test index 6996ff69..ce38dbdf 100644 --- a/tests/test_index.nf.test +++ b/tests/test_index.nf.test @@ -18,7 +18,246 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 161 } + { assert workflow.trace.succeeded().size() == 161 }, + + { assert snapshot( + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") + ).match("bowtie_index") }, + + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), + path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") + ).match("multiqc") }, + + { assert snapshot( + path("$outputDir/untar/bowtie_index/genome.rev.2.ebwt"), + path("$outputDir/untar/bowtie_index/genome.2.ebwt"), + path("$outputDir/untar/bowtie_index/genome.1.ebwt"), + path("$outputDir/untar/bowtie_index/genome.3.ebwt"), + path("$outputDir/untar/bowtie_index/genome.4.ebwt"), + path("$outputDir/untar/bowtie_index/genome.rev.1.ebwt") + ).match("untar") }, + + { assert snapshot( + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists() + ).match("genome_quant") }, + + { assert snapshot( + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop.tsv").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop.gff").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists(), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists() + ).match("mirna_quant") }, + + { assert snapshot( + path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip").exists() + ).match("fastqc") }, + + { assert snapshot( + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") + ).match("mirtrace") }, + ) } diff --git a/tests/test_index.nf.test.snap b/tests/test_index.nf.test.snap new file mode 100644 index 00000000..3169c975 --- /dev/null +++ b/tests/test_index.nf.test.snap @@ -0,0 +1,292 @@ +{ + "bowtie_index": { + "content": [ + "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", + "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", + "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", + "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", + "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", + "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", + "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", + "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", + "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", + "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", + "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", + "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-20T20:50:18.193559565" + }, + "mirtrace": { + "content": [ + "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", + "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", + "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", + "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", + "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", + "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", + "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638", + "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", + "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", + "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", + "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", + "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", + "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", + "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", + "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8", + "Clone1_N1.fastp.fasta:md5,e297dfa46353946d6c140e4513dd4525", + "Clone9_N1.fastp.fasta:md5,63a17d136548fc98f34c8d98006cc7da", + "Control_N3.fastp.fasta:md5,d9980a598ece252e19d6c9ebefd51861", + "Control_N1.fastp.fasta:md5,e964e05ce2c93937a8e76602f2e08150", + "Clone9_N2.fastp.fasta:md5,b1ca39e6e1e75ee7d654d9ccfb35e906", + "Control_N2.fastp.fasta:md5,8cefbc494be7b363b19c10b8c00366b2", + "Clone1_N3.fastp.fasta:md5,4012282462dde0750f09cec883304cc3", + "Clone9_N3.fastp.fasta:md5,f733e20eb8d2a2009ca82464e8ccb148" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-20T20:50:30.083738998" + }, + "genome_quant": { + "content": [ + "Control_N2_mature_hairpin_genome.sorted.flagstat:md5,b0d42e94b2e0e026cd32a88dce40722c", + "Control_N2_mature_hairpin_genome.sorted.stats:md5,1222b755feaf406ecea3f2abb35a737c", + "Control_N2_mature_hairpin_genome.sorted.idxstats:md5,b6da32ce230fdeab39f3c4d5dcf41a3a", + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-20T20:50:19.817165699" + }, + "software_versions": { + "content": [ + "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, UNTAR_BOWTIE_INDEX={untar=1.3}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-20T20:50:18.088216994" + }, + "fastqc": { + "content": [ + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-20T20:50:25.856996924" + }, + "untar": { + "content": [ + "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", + "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", + "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", + "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", + "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", + "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-20T20:50:19.213915527" + }, + "multiqc": { + "content": [ + "fastqc-status-check-heatmap.txt:md5,30f55902420433a11971d36956e8576e", + "fastp_filtered_reads_plot.txt:md5,0af4d3cfbf463f33b2b88cdfd69909ac", + "fastqc_overrepresented_sequences_plot.txt:md5,d861a4a956a3023efa19b1259d8665b2", + true, + "fastqc_sequence_counts_plot-1.txt:md5,37d8ae6c5734eb2679e65e46c9af9101", + "mirtrace_complexity_plot.txt:md5,5f78d6f559a9642e68e1fd74ac2c11ca", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", + "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", + "samtools-stats-dp.txt:md5,0f88cdcc523ea239c2dd7e1e2decec36", + "fastqc_sequence_length_distribution_plot.txt:md5,13f72b3be854c74cd7b5176ca0583770", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "fastqc_sequence_duplication_levels_plot-1.txt:md5,06a4162d4787883b1f39a1b9acb7bb91", + "fastqc_per_base_sequence_quality_plot-1.txt:md5,6a0df664a369ee216412f0033ed3a042", + true, + "fastqc_per_base_n_content_plot-1.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "fastqc_per_base_n_content_plot.txt:md5,fb8a49467d1679dbf716e1f00c1f25e5", + "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,b1481a9fbf5ea541b39aed99b51d616f", + "fastqc_per_sequence_quality_scores_plot.txt:md5,38dbd6509de7f1beac17e44acb8336be", + "mirtrace_qc_plot.txt:md5,c436d017382baed6617fc3c1ad8ab41d", + "fastqc_per_sequence_quality_scores_plot-1.txt:md5,69f4459318311103fe71a5d1d3b2c076", + "mirtrace_length_plot.txt:md5,2366f10eb8bd3c32d2b35e2df20c786c", + true, + "fastqc_overrepresented_sequences_plot-1.txt:md5,1de000de50cc7516bb9d996def14c6eb", + "fastqc-status-check-heatmap-1.txt:md5,e64c353797e6dc057d10b3194ca6b20d", + "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", + "mirtrace_rna_categories_plot.txt:md5,8665376e2a123e1661f82cbbee54789f", + "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", + "samtools_alignment_plot.txt:md5,ac24d7f3bf5858e7550d2f93446137e1", + "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", + true, + "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + true, + true, + "fastqc_adapter_content_plot.txt:md5,86a0f478fd3e690ef5132d08bf4e7625", + "fastqc_sequence_duplication_levels_plot.txt:md5,88b0babe77f623547e8af664791ef2d0", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,539883757ae5bf731da93fe0568022e9", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,ed7205b9c46d5f431c5b3bf499a673a1", + "fastqc_adapter_content_plot-1.txt:md5,71ba0983a71f3a833526ab83a985d072", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,a8387a3e6b350acd16bb0ed5a43949d8", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3e9c1a7204c12d9c1b3b53342cf61840", + true, + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,efa8123c9ad43f99a6fba671f50322ca" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-20T20:50:18.947900403" + }, + "mirna_quant": { + "content": [ + "Control_N1_mature_hairpin.sorted.stats:md5,feb69ad2f8bbc527e39502a297f08abd", + "Control_N1_mature_hairpin.sorted.idxstats:md5,e1f455195f1cb42a1d1e58770aaeb2b4", + "Clone1_N3_mature_hairpin.sorted.flagstat:md5,6f14ec4cd502c0eb213b1905b4568a76", + "Clone9_N2_mature_hairpin.sorted.stats:md5,7bb8654d44dac245aec6aa045250628a", + "Clone9_N3_mature_hairpin.sorted.flagstat:md5,efc65cb620ca139b19967e12f13ba007", + true, + true, + "Control_N1_mature_hairpin.sorted.flagstat:md5,41769a400a176ea78432749f07f80fda", + true, + "Clone9_N1_mature_hairpin.sorted.stats:md5,155f327a9be0afa9584ec426826b5457", + true, + "Control_N2_mature_hairpin.sorted.stats:md5,1195dd51f77e338db83dc66476ac7c5f", + true, + "Control_N3_mature_hairpin.sorted.idxstats:md5,2c44710ce63bdebb12d64c729ef338b0", + true, + true, + "Clone1_N1_mature_hairpin.sorted.idxstats:md5,0bca2d01f734128f3c11cf2697433048", + "Clone9_N3_mature_hairpin.sorted.idxstats:md5,9523d29d411c2efb0a1756355230fa98", + "Control_N2_mature_hairpin.sorted.idxstats:md5,8859b6e432cef8b24d5fb258a06aaabe", + "Clone9_N2_mature_hairpin.sorted.flagstat:md5,663ae0bb8b29d1e1c3d75ef5df1015a4", + "Clone9_N1_mature_hairpin.sorted.flagstat:md5,3e4b295b54df05c438603edaa53123b1", + "Control_N3_mature_hairpin.sorted.flagstat:md5,f3df866b94dc6ef355b01f22047aaf4f", + true, + true, + true, + "Clone9_N3_mature_hairpin.sorted.stats:md5,9f61c028bb1c92667e31093156ada662", + "Clone1_N1_mature_hairpin.sorted.stats:md5,bd02cb15e666054edecc89d392d72902", + "Clone9_N2_mature_hairpin.sorted.idxstats:md5,04b1c0ea4f133b5ee9086eec1f4077e7", + "Clone1_N3_mature_hairpin.sorted.stats:md5,471db325d8ccd1fe787b5dd91dccf487", + true, + "Control_N2_mature_hairpin.sorted.flagstat:md5,2605548b5ab1e6ad6b5cf88ea0030909", + "Clone9_N1_mature_hairpin.sorted.idxstats:md5,238b462a2418d545418c0b3a28029bdf", + true, + "Control_N3_mature_hairpin.sorted.stats:md5,2f2249c537451d1f72dfe298f16093ac", + true, + true, + "Clone1_N1_mature_hairpin.sorted.flagstat:md5,8d0c785fec7b300200863c68b158444c", + true, + true, + "Clone1_N3_mature_hairpin.sorted.idxstats:md5,5b6cd8d5784c387d2649f18499a17c6e", + true, + "Clone1_N1_mature.sorted.stats:md5,9c42ffda181ca24ab076efc16fcfd4b3", + "Clone1_N3_mature.sorted.idxstats:md5,805f115ac4d9c8033908bafaba6c92fb", + "Clone9_N2_mature.sorted.stats:md5,fb8c403012481dafb895013c555f6d85", + "Control_N2_mature.sorted.stats:md5,ef5935898e3ca45d898053af335d1dfb", + "Control_N3_mature.sorted.flagstat:md5,2831f55bccbcf666d1c313ef377bcb30", + true, + true, + "Clone9_N3_mature.sorted.stats:md5,23b012dd60ea6dcec5cedb5a73ffc792", + true, + "Clone1_N3_mature.sorted.flagstat:md5,67fc6ba8516d4e5b3ed2a62febc92f0a", + "Clone9_N1_mature.sorted.idxstats:md5,c6eb22f3ff675e422d065375279150b2", + true, + "Control_N1_mature.sorted.stats:md5,b4ffb3a7623e32420def4d3470a326ab", + "Control_N1_mature.sorted.idxstats:md5,847bc5c6ef44e1f9754e47e648a5ef98", + "Clone9_N2_mature.sorted.flagstat:md5,247e02da50509fc1b3c5b35001922a8d", + "Control_N2_mature.sorted.flagstat:md5,c8742d1b49535ff815c2def66cba681e", + true, + true, + true, + "Control_N2_mature.sorted.idxstats:md5,12388de965d69b6102b62bc9cdf27e85", + true, + "Clone9_N1_mature.sorted.flagstat:md5,014b846757652783ff3f954a966b8a1b", + true, + true, + "Clone9_N3_mature.sorted.idxstats:md5,dee54e8e22dfca24acc290bf89a05cd4", + "Clone9_N2_mature.sorted.idxstats:md5,c9643d610de2f4d449a876e41dcab872", + "Clone9_N3_mature.sorted.flagstat:md5,4f60cfd3527e91df204253f9f1aebfcd", + "Control_N3_mature.sorted.idxstats:md5,5fb7b46915043bd3c947a37afc3e8075", + true, + true, + "Clone1_N1_mature.sorted.idxstats:md5,77ed64ddd23cf07340b65c04559d4726", + true, + "Clone1_N1_mature.sorted.flagstat:md5,f138a532bc7dab94f7cf4b4a4e5e23e5", + "Control_N3_mature.sorted.stats:md5,ff9dab4d3220aa44cdc80ea2fc311823", + "Clone1_N3_mature.sorted.stats:md5,e8feced949af44c8e5d31523b12122b9", + true, + true, + "Control_N1_mature.sorted.flagstat:md5,16318a574fe410b81c0e2cdf0dfa3c97", + "Clone9_N1_mature.sorted.stats:md5,02184884c17c8730f4df9e1a6144bbdc", + "mirna.tsv:md5,1f840afe7ab68eac73feaaad321b64f6", + true, + true, + "mirtop_rawData.tsv:md5,774410dd2cf1e5be83bf8d6e1e8b96b0", + true, + "Clone1_N3.fastp_trimmed.fastq.gz:md5,2e395240c74b3870efe03dc329d8bad8", + "Control_N1.fastp_trimmed.fastq.gz:md5,2f09082eb68a8f1dc308050e330887ec", + "Control_N3.fastp_trimmed.fastq.gz:md5,342368a6e6acdaf0ae9379676b6d07f0", + "Clone9_N1.fastp_trimmed.fastq.gz:md5,115cf0c346a93a47ba782c5724b4f090", + "Clone1_N1.fastp_trimmed.fastq.gz:md5,14a2590e663dbde105780726c2173c25", + "Clone9_N2.fastp_trimmed.fastq.gz:md5,c922ec95a4b84d806dd2054ff0f9cab7", + "Clone9_N3.fastp_trimmed.fastq.gz:md5,67cf9a7d2fa431f0e772391ed1651f93", + "Control_N2.fastp_trimmed.fastq.gz:md5,d6e607edcb3d71c546ce8fdfb18e3999", + "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", + "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", + "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + true, + true, + true, + true, + true, + true, + true, + true, + "hairpin_log2CPM_sample_distances.txt:md5,b19fa1d9f821fc8e2c0e9f34f76b5479", + true, + true, + true, + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T17:43:32.069747201" + } +} \ No newline at end of file diff --git a/tests/test_mirgenedb.nf.test b/tests/test_mirgenedb.nf.test index 19636057..6a4f243e 100644 --- a/tests/test_mirgenedb.nf.test +++ b/tests/test_mirgenedb.nf.test @@ -1,3 +1,4 @@ + nextflow_pipeline { name "Test Workflow main.nf - test_mirgenedb" @@ -18,7 +19,241 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 193 } + { assert workflow.trace.succeeded().size() == 193 }, + + { assert snapshot( + path("$outputDir/mirna_quant/reference/hsa-hg38-pri-30-30.fas_igenome.fa"), + path("$outputDir/mirna_quant/reference/hsa_igenome.fa"), + path("$outputDir/mirna_quant/reference/hsa-hg38-pri-30-30.fas_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hsa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists() + ).match("mirna_quant") }, + + { assert snapshot( + path("$outputDir/bowtie_index/genome/genome.3.ebwt"), + path("$outputDir/bowtie_index/genome/genome.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.4.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.edited.fa"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt") + ).match("bowtie_index") }, + + { assert snapshot( + path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip").exists() + ).match("fastqc") }, + + { assert snapshot( + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.stats") + ).match("genome_quant") }, + + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), + path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") + ).match("multiqc") }, + ) } diff --git a/tests/test_mirgenedb.nf.test.snap b/tests/test_mirgenedb.nf.test.snap new file mode 100644 index 00000000..375fabc4 --- /dev/null +++ b/tests/test_mirgenedb.nf.test.snap @@ -0,0 +1,275 @@ +{ + "bowtie_index": { + "content": [ + "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", + "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", + "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", + "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", + "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", + "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", + "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", + "fasta_bidx.3.ebwt:md5,ff4179d03d07954bc2c4e9e3db53cc84", + "fasta_bidx.4.ebwt:md5,5f58f8d33f5f4ad024fe5d5bed359e70", + "fasta_bidx.1.ebwt:md5,058b4869546dd035b4a0c04f5f88e2a0", + "fasta_bidx.rev.1.ebwt:md5,4ad69edd9799cc0a962fb4227336fbfb", + "fasta_bidx.2.ebwt:md5,f2a632771f4d91546b7d72eb02a074be", + "fasta_bidx.rev.2.ebwt:md5,f46776adf134dbf7b15a18ecb6810b05", + "fasta_bidx.1.ebwt:md5,7f642e502a03af140cc9defea6c5fbad", + "fasta_bidx.2.ebwt:md5,990abde7202805872f56781abfce9da1", + "fasta_bidx.3.ebwt:md5,f132742aec53cedb06ca87d289f9f4a2", + "fasta_bidx.rev.1.ebwt:md5,34feb7692da8d4752343cf327e1f4446", + "fasta_bidx.rev.2.ebwt:md5,ea6d4ad4a6fbc394e189ba95c38eaad0", + "fasta_bidx.4.ebwt:md5,70977c4174dd54d5715e24cbe148686c" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T15:55:30.30966024" + }, + "genome_quant": { + "content": [ + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + "Clone9_N1_mature_hairpin_genome.sorted.flagstat:md5,6a8ad3be2ca0fa924fd32a04293d4ce4", + "Clone1_N1_mature_hairpin_genome.sorted.flagstat:md5,5bb521c495f1c450835299b1eb88dc84", + "Control_N2_mature_hairpin_genome.sorted.idxstats:md5,8fe506f0e0fb6fdec63ec3ac46088971", + "Clone9_N1_mature_hairpin_genome.sorted.idxstats:md5,aa37c5da7c2b4505ce58c3a21f97121c", + "Clone1_N3_mature_hairpin_genome.sorted.idxstats:md5,55fca6b9d8263d72d1ecd48d9dcb6cd4", + "Control_N1_mature_hairpin_genome.sorted.flagstat:md5,df2a57ac3b36f5d40793d3105a4bb2d1", + "Control_N3_mature_hairpin_genome.sorted.idxstats:md5,33ff4580ba9a6c28eb5ae94519ebba3d", + "Clone9_N3_mature_hairpin_genome.sorted.flagstat:md5,c8756a6359a58edfca350a288129e87c", + "Clone1_N1_mature_hairpin_genome.sorted.idxstats:md5,d92f9eae7657418858e6d2b69436f74f", + "Control_N1_mature_hairpin_genome.sorted.idxstats:md5,a11f543771cea6b383fb596f60e998c3", + "Clone9_N2_mature_hairpin_genome.sorted.flagstat:md5,c9ea13138a4ade6bb64ac5de54bc2738", + "Clone9_N2_mature_hairpin_genome.sorted.idxstats:md5,6f07962963e26663dc09e72eb60c887f", + "Clone9_N3_mature_hairpin_genome.sorted.idxstats:md5,730cc6e2f92875f53ba5abaee4fc7a92", + "Control_N3_mature_hairpin_genome.sorted.flagstat:md5,047445077b03d7db3e7f5a3d5d162a1a", + "Control_N2_mature_hairpin_genome.sorted.flagstat:md5,b561e1e2e059cf4a8d156d2878d14638", + "Clone9_N3_mature_hairpin_genome.sorted.stats:md5,d73bffca2d2e685198bb1758c8e3e37c", + "Clone1_N3_mature_hairpin_genome.sorted.flagstat:md5,e21a3e140c55792fb394ddc7fc374d29", + "Clone9_N2_mature_hairpin_genome.sorted.stats:md5,77ddc325e6f6b6cf872bc490b31d037d", + "Control_N2_mature_hairpin_genome.sorted.stats:md5,c1a6335191f99e05d41738c78f5d2498", + "Clone9_N1_mature_hairpin_genome.sorted.stats:md5,26c8e55e56641f2d4387a37b099ff0c2", + "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,03d3f6227829c80c0e29cb49df9b6a27", + "Control_N1_mature_hairpin_genome.sorted.stats:md5,6a53b78cc7e4ca2338c76095af080151", + "Clone1_N3_mature_hairpin_genome.sorted.stats:md5,072c74c558a972d462042fb4e3804209", + "Control_N3_mature_hairpin_genome.sorted.stats:md5,359d0ab9cc2b45b38efb7609cb80e463" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T17:57:17.873520964" + }, + "software_versions": { + "content": [ + "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_GENOME={bowtie=1.3.1}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T15:55:13.060125336" + }, + "fastqc": { + "content": [ + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T17:57:13.983711958" + }, + "multiqc": { + "content": [ + "fastqc-status-check-heatmap.txt:md5,30f55902420433a11971d36956e8576e", + "fastp_filtered_reads_plot.txt:md5,0af4d3cfbf463f33b2b88cdfd69909ac", + "fastqc_overrepresented_sequences_plot.txt:md5,d861a4a956a3023efa19b1259d8665b2", + true, + "fastqc_sequence_counts_plot-1.txt:md5,37d8ae6c5734eb2679e65e46c9af9101", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", + "multiqc_citations.txt:md5,57db2426be011862828d18f767d25b57", + "samtools-stats-dp.txt:md5,90d663100472e8b52c2c04c9ee28babf", + "fastqc_sequence_length_distribution_plot.txt:md5,13f72b3be854c74cd7b5176ca0583770", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "fastqc_sequence_duplication_levels_plot-1.txt:md5,06a4162d4787883b1f39a1b9acb7bb91", + "fastqc_per_base_sequence_quality_plot-1.txt:md5,6a0df664a369ee216412f0033ed3a042", + true, + "fastqc_per_base_n_content_plot-1.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "fastqc_per_base_n_content_plot.txt:md5,fb8a49467d1679dbf716e1f00c1f25e5", + "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,b1481a9fbf5ea541b39aed99b51d616f", + "fastqc_per_sequence_quality_scores_plot.txt:md5,38dbd6509de7f1beac17e44acb8336be", + "fastqc_per_sequence_quality_scores_plot-1.txt:md5,69f4459318311103fe71a5d1d3b2c076", + true, + "fastqc_overrepresented_sequences_plot-1.txt:md5,1de000de50cc7516bb9d996def14c6eb", + "fastqc-status-check-heatmap-1.txt:md5,e64c353797e6dc057d10b3194ca6b20d", + "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", + "samtools_alignment_plot.txt:md5,07766860ac4d8739fcec6b5b51289b57", + true, + "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", + "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", + "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "fastqc_adapter_content_plot.txt:md5,86a0f478fd3e690ef5132d08bf4e7625", + "fastqc_sequence_duplication_levels_plot.txt:md5,88b0babe77f623547e8af664791ef2d0", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,539883757ae5bf731da93fe0568022e9", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,ed7205b9c46d5f431c5b3bf499a673a1", + "fastqc_adapter_content_plot-1.txt:md5,71ba0983a71f3a833526ab83a985d072", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,a8387a3e6b350acd16bb0ed5a43949d8", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3e9c1a7204c12d9c1b3b53342cf61840", + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,efa8123c9ad43f99a6fba671f50322ca" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T17:57:21.712642814" + }, + "mirna_quant": { + "content": [ + "hsa-hg38-pri-30-30.fas_igenome.fa:md5,0330f80966b98ef9b300db0b312c422d", + "hsa_igenome.fa:md5,f8a652b0a51db6ce518f7cdba06c3c01", + "hsa-hg38-pri-30-30.fas_igenome.fa_idx.fa:md5,f550596c4dc78658f1aa438c3f2432f1", + "hsa_igenome.fa_idx.fa:md5,f8a652b0a51db6ce518f7cdba06c3c01", + "Control_N2.fastp_trimmed.fastq.gz:md5,d6e607edcb3d71c546ce8fdfb18e3999", + "Clone1_N3.fastp_trimmed.fastq.gz:md5,2e395240c74b3870efe03dc329d8bad8", + "Clone9_N3.fastp_trimmed.fastq.gz:md5,67cf9a7d2fa431f0e772391ed1651f93", + "Clone9_N2.fastp_trimmed.fastq.gz:md5,c922ec95a4b84d806dd2054ff0f9cab7", + "Control_N1.fastp_trimmed.fastq.gz:md5,2f09082eb68a8f1dc308050e330887ec", + "Clone1_N1.fastp_trimmed.fastq.gz:md5,14a2590e663dbde105780726c2173c25", + "Clone9_N1.fastp_trimmed.fastq.gz:md5,115cf0c346a93a47ba782c5724b4f090", + "Control_N3.fastp_trimmed.fastq.gz:md5,342368a6e6acdaf0ae9379676b6d07f0", + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + "Clone9_N1_mature.sorted.stats:md5,96b82a0250469c1754abddd4c9b121f2", + "Clone9_N2_mature.sorted.flagstat:md5,e705ff2fb2aff90722587e4ef2574d47", + "Control_N2_mature.sorted.flagstat:md5,26eac956af9432cb43344d75001e134b", + "Clone1_N3_mature.sorted.flagstat:md5,b66820feb3fb642aa1d3812f96c17a8f", + "Control_N1_mature.sorted.idxstats:md5,b7a382b1d0f5cba6cb94b3b5a6b18f84", + "Control_N3_mature.sorted.stats:md5,926dbbacb28c0c79a9129dfe13b8ea46", + "Control_N3_mature.sorted.flagstat:md5,ebc0ab77211c4c0537f2dae119c61ca2", + "Clone9_N3_mature.sorted.stats:md5,20ed6d356eaa16e0820afb682505ef8e", + "Control_N3_mature.sorted.idxstats:md5,313845385850985d36906780a932f5e2", + "Clone9_N1_mature.sorted.idxstats:md5,8302f401476f5c8fee3333e1c742c05e", + "Control_N1_mature.sorted.stats:md5,2a5fce73b26297bfce12d75b1e59b205", + "Clone1_N1_mature.sorted.idxstats:md5,f391c89a5631b2f2c2d31ebe07fb47d0", + "Clone9_N2_mature.sorted.idxstats:md5,fa0c2e4129cdf8d4b1db81040f488b06", + "Control_N2_mature.sorted.idxstats:md5,6a40778e06c327a4bd7b4b8288839391", + "Control_N1_mature.sorted.flagstat:md5,f8df7690d20014518f47dc2fe39debec", + "Clone1_N1_mature.sorted.flagstat:md5,e5dfab2690df9cb96aec5889ad008604", + "Clone1_N3_mature.sorted.stats:md5,8c5829865ae9fbfddae57947cb6c9519", + "Clone1_N3_mature.sorted.idxstats:md5,f1c77fac455e51e5a3d41520c4fd7b94", + "Clone9_N2_mature.sorted.stats:md5,d1a72eb2ee8d515979e3d9c6aca36841", + "Clone9_N1_mature.sorted.flagstat:md5,adf40ba27907b6ef726d6c5923a731b9", + "Clone9_N3_mature.sorted.idxstats:md5,1f11006d861191605278b6e5fdfa3d9a", + "Control_N2_mature.sorted.stats:md5,daab0b0c64f6f43ad16f1bcf269d397f", + "Clone9_N3_mature.sorted.flagstat:md5,a027a77c3750bfb1172ce1dc3b3c2759", + "Clone1_N1_mature.sorted.stats:md5,c0756996051adc8d1bd0d0b60fd0855b", + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + "Clone9_N1_mature_hairpin.sorted.idxstats:md5,f3ed5bf23f73d41c42d3da0bf30f89ea", + "Clone1_N1_mature_hairpin.sorted.idxstats:md5,cc9d2c4ad6d7e05e4a05c8006d64ac6d", + "Control_N3_mature_hairpin.sorted.stats:md5,7f263ca41f6fe3a48afae87ca4d4bb5f", + "Clone9_N2_mature_hairpin.sorted.flagstat:md5,ab147350da763f38aaddb0b058d2eb1e", + "Clone9_N2_mature_hairpin.sorted.stats:md5,9665ed98a7d4ef1ae49b572008a9ab5d", + "Clone9_N2_mature_hairpin.sorted.idxstats:md5,07ed767bcfd4fa6fad9c78765e790064", + "Clone1_N3_mature_hairpin.sorted.flagstat:md5,614588858f8e91665e913785c422ce42", + "Clone9_N3_mature_hairpin.sorted.stats:md5,98a332aa9c51669ad5aa39429e4e386a", + "Clone9_N1_mature_hairpin.sorted.stats:md5,91bb004f5271b4c507bef7d274df3d61", + "Control_N1_mature_hairpin.sorted.idxstats:md5,79dc5e82ff88e7379c893549224cd87f", + "Clone1_N1_mature_hairpin.sorted.flagstat:md5,ba7fd1aa5c0ed1bb161d1f4278926040", + "Control_N2_mature_hairpin.sorted.idxstats:md5,76a470476116128573764db2399d8565", + "Control_N1_mature_hairpin.sorted.stats:md5,546c01ab7193d65418db5e11ab57f8c6", + "Control_N3_mature_hairpin.sorted.flagstat:md5,f5e2a68427234f7f4fb6f28227f61e02", + "Clone1_N3_mature_hairpin.sorted.stats:md5,29aa9e13aa7d7c95ac2aabd67e49482a", + "Control_N2_mature_hairpin.sorted.stats:md5,14064d698b3f709b31b8d7022c9f07cf", + "Control_N3_mature_hairpin.sorted.idxstats:md5,b35b14f7dfc8fc4a7a757bf0596e0e0f", + "Clone9_N1_mature_hairpin.sorted.flagstat:md5,678f4f9e98c3e1fcc5af54e8dd06fbbc", + "Clone1_N1_mature_hairpin.sorted.stats:md5,105a9a3726ab313c5845c70042fdffff", + "Clone1_N3_mature_hairpin.sorted.idxstats:md5,32e53141026ee40748d8472be8bb561a", + "Clone9_N3_mature_hairpin.sorted.idxstats:md5,c0364e7a3b43606b8530adaea02a90b3", + "Clone9_N3_mature_hairpin.sorted.flagstat:md5,e2a4383981c36024c09c99bcc45d8cc2", + "Control_N1_mature_hairpin.sorted.flagstat:md5,1dc7b98f0014a99a20de7c09a6b95340", + "Control_N2_mature_hairpin.sorted.flagstat:md5,c830a70e5badf24c4c2067d5d856853e", + true, + true, + "hairpin_log2CPM_sample_distances.txt:md5,ee28abcd0c9c3c05d22453e1039fe6a1", + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T17:57:09.190802792" + } +} \ No newline at end of file diff --git a/tests/test_no_genome.nf.test b/tests/test_no_genome.nf.test index 2805ce3c..bd38e938 100644 --- a/tests/test_no_genome.nf.test +++ b/tests/test_no_genome.nf.test @@ -18,7 +18,277 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 147 } + { assert workflow.trace.succeeded().size() == 147 }, + + { assert snapshot( + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") + ).match("bowtie_index") }, + + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), + path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") + ).match("multiqc") }, + + { assert snapshot( + path("$outputDir/mirna_quant/bam/seqcluster/Control_N3_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N3_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/Control_N1_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N2_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N3_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N1_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/Control_N2_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N1_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N2_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N1_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N1_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N3_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N1_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N3_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N3_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N2_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N1_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N1_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N3_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N2_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N2_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N3_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N3_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N1_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N3_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N1_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N3_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone1_N1_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N1_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N2_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone1_N3_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N2_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop.tsv").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop.gff").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists(), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists() + ).match("mirna_quant") }, + + { assert snapshot( + path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip").exists() + ).match("fastqc") }, + + { assert snapshot( + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") + ).match("mirtrace") }, + ) } diff --git a/tests/test_no_genome.nf.test.snap b/tests/test_no_genome.nf.test.snap new file mode 100644 index 00000000..6522d674 --- /dev/null +++ b/tests/test_no_genome.nf.test.snap @@ -0,0 +1,311 @@ +{ + "bowtie_index": { + "content": [ + "fasta_bidx.3.ebwt:md5,cccaad86d0d5e5f3c1d4ca3a700ee980", + "fasta_bidx.1.ebwt:md5,9935201150ff358248380e07219fe093", + "fasta_bidx.rev.1.ebwt:md5,5e75ec9fb284ba316b3982a93f4ded49", + "fasta_bidx.rev.2.ebwt:md5,ba8e745f11b3d28240a78efd5bf2a7b0", + "fasta_bidx.4.ebwt:md5,96e2e8ec9f02d324d845e0708ff4b552", + "fasta_bidx.2.ebwt:md5,9cf18dd788535404d7fd6a62450d2ce0", + "fasta_bidx.3.ebwt:md5,a6d3abdddbf80cb9b2c97bbd7bc1f084", + "fasta_bidx.1.ebwt:md5,a2162fb747e95535ea5a67023b8961cf", + "fasta_bidx.rev.1.ebwt:md5,27578696198a61b0a3f783802823337e", + "fasta_bidx.rev.2.ebwt:md5,726c60d9a0108739ba9b61774bc39633", + "fasta_bidx.4.ebwt:md5,62e35549f28a1a85ccaf35858b1726aa", + "fasta_bidx.2.ebwt:md5,876ebed9375cda6f248dfc940308fa5e" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T16:07:40.616713823" + }, + "mirtrace": { + "content": [ + "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", + "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", + "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", + "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", + "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", + "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", + "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638", + "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", + "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", + "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", + "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", + "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", + "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", + "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", + "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8", + "Clone1_N1.fastp.fasta:md5,e297dfa46353946d6c140e4513dd4525", + "Clone9_N1.fastp.fasta:md5,63a17d136548fc98f34c8d98006cc7da", + "Control_N3.fastp.fasta:md5,d9980a598ece252e19d6c9ebefd51861", + "Control_N1.fastp.fasta:md5,e964e05ce2c93937a8e76602f2e08150", + "Clone9_N2.fastp.fasta:md5,b1ca39e6e1e75ee7d654d9ccfb35e906", + "Control_N2.fastp.fasta:md5,8cefbc494be7b363b19c10b8c00366b2", + "Clone1_N3.fastp.fasta:md5,4012282462dde0750f09cec883304cc3", + "Clone9_N3.fastp.fasta:md5,f733e20eb8d2a2009ca82464e8ccb148" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T16:10:10.373656708" + }, + "software_versions": { + "content": [ + "{BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T16:07:40.61071488" + }, + "fastqc": { + "content": [ + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T16:09:02.324824552" + }, + "multiqc": { + "content": [ + "fastqc-status-check-heatmap.txt:md5,30f55902420433a11971d36956e8576e", + "fastp_filtered_reads_plot.txt:md5,0af4d3cfbf463f33b2b88cdfd69909ac", + "fastqc_overrepresented_sequences_plot.txt:md5,d861a4a956a3023efa19b1259d8665b2", + true, + "fastqc_sequence_counts_plot-1.txt:md5,37d8ae6c5734eb2679e65e46c9af9101", + "mirtrace_complexity_plot.txt:md5,5f78d6f559a9642e68e1fd74ac2c11ca", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", + "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", + "samtools-stats-dp.txt:md5,951e248c4dce68d25e14f0c79ef36e2e", + "fastqc_sequence_length_distribution_plot.txt:md5,13f72b3be854c74cd7b5176ca0583770", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "fastqc_sequence_duplication_levels_plot-1.txt:md5,06a4162d4787883b1f39a1b9acb7bb91", + "fastqc_per_base_sequence_quality_plot-1.txt:md5,6a0df664a369ee216412f0033ed3a042", + true, + "fastqc_per_base_n_content_plot-1.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + "fastqc_per_base_n_content_plot.txt:md5,fb8a49467d1679dbf716e1f00c1f25e5", + "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,b1481a9fbf5ea541b39aed99b51d616f", + "fastqc_per_sequence_quality_scores_plot.txt:md5,38dbd6509de7f1beac17e44acb8336be", + "mirtrace_qc_plot.txt:md5,c436d017382baed6617fc3c1ad8ab41d", + "fastqc_per_sequence_quality_scores_plot-1.txt:md5,69f4459318311103fe71a5d1d3b2c076", + "mirtrace_length_plot.txt:md5,2366f10eb8bd3c32d2b35e2df20c786c", + true, + "fastqc_overrepresented_sequences_plot-1.txt:md5,1de000de50cc7516bb9d996def14c6eb", + "fastqc-status-check-heatmap-1.txt:md5,e64c353797e6dc057d10b3194ca6b20d", + "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", + "mirtrace_rna_categories_plot.txt:md5,8665376e2a123e1661f82cbbee54789f", + "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", + "samtools_alignment_plot.txt:md5,e4335c4194bffb41df16619f3abfe705", + "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", + true, + "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", + true, + true, + "fastqc_adapter_content_plot.txt:md5,86a0f478fd3e690ef5132d08bf4e7625", + "fastqc_sequence_duplication_levels_plot.txt:md5,88b0babe77f623547e8af664791ef2d0", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,539883757ae5bf731da93fe0568022e9", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,ed7205b9c46d5f431c5b3bf499a673a1", + "fastqc_adapter_content_plot-1.txt:md5,71ba0983a71f3a833526ab83a985d072", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,a8387a3e6b350acd16bb0ed5a43949d8", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,3e9c1a7204c12d9c1b3b53342cf61840", + true, + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,efa8123c9ad43f99a6fba671f50322ca" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T16:07:41.27780496" + }, + "mirna_quant": { + "content": [ + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + "Control_N1_mature_hairpin.sorted.stats:md5,9eb22683401f87e60cbc0cc73b39b8b7", + "Control_N1_mature_hairpin.sorted.idxstats:md5,6ed8ee411919ec9baa5034679be63770", + "Clone1_N3_mature_hairpin.sorted.flagstat:md5,40449964287854e14984545f4007677c", + "Clone9_N2_mature_hairpin.sorted.stats:md5,925c282fdcd53d9b16e3c89840506daa", + true, + "Clone9_N3_mature_hairpin.sorted.flagstat:md5,43adb927ee6032297e95fedc5b080ca1", + true, + true, + true, + "Control_N1_mature_hairpin.sorted.flagstat:md5,94856ef0ef3e2944df1bddc31a118121", + true, + "Clone9_N1_mature_hairpin.sorted.stats:md5,fa18dddebf8b084542858f2c13342c2d", + true, + "Control_N2_mature_hairpin.sorted.stats:md5,0f618f0e64bd16ed4858c9012b7adf87", + true, + "Control_N3_mature_hairpin.sorted.idxstats:md5,0981f7a524ff0036b2d77c97147f0f0e", + true, + true, + true, + "Clone1_N1_mature_hairpin.sorted.idxstats:md5,d54f57a896c7b7b5824e3af5b51f3fd2", + "Clone9_N3_mature_hairpin.sorted.idxstats:md5,361861d00aa0086eb1aa8bacc616db60", + true, + "Control_N2_mature_hairpin.sorted.idxstats:md5,364ab0efe73b5369e362bf12ed738009", + "Clone9_N2_mature_hairpin.sorted.flagstat:md5,5f3be7d1cf5db0ac22b1e4bbbc89460f", + true, + "Clone9_N1_mature_hairpin.sorted.flagstat:md5,718c6b942e1171211326118f4877c4ad", + true, + "Control_N3_mature_hairpin.sorted.flagstat:md5,dca2071057d621f04d3c88c5fcc061eb", + true, + true, + true, + true, + "Clone9_N3_mature_hairpin.sorted.stats:md5,e414a9e5b8a6e737cdd5aacaaaa40da8", + "Clone1_N1_mature_hairpin.sorted.stats:md5,15987963f6d2a224565663ae49a2bb19", + "Clone9_N2_mature_hairpin.sorted.idxstats:md5,416c4f9aef6f2c79c329f477044e6485", + "Clone1_N3_mature_hairpin.sorted.stats:md5,8f0cb54dcf9604c6ea3cfc860b483725", + true, + "Control_N2_mature_hairpin.sorted.flagstat:md5,886085252cd07b0bbe8073be4549c719", + "Clone9_N1_mature_hairpin.sorted.idxstats:md5,2c376fd533eaa5bfd321657e8cdfc9f1", + true, + "Control_N3_mature_hairpin.sorted.stats:md5,55cac79ae09a6147ffba190d6115bfa4", + true, + true, + "Clone1_N1_mature_hairpin.sorted.flagstat:md5,b2e8eb3b3d10a01a3794e2410c3ba270", + true, + true, + true, + "Clone1_N3_mature_hairpin.sorted.idxstats:md5,a2457f5571563ecc03c4d9834fa75da0", + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + "Clone1_N1_mature.sorted.stats:md5,9c42ffda181ca24ab076efc16fcfd4b3", + "Clone1_N3_mature.sorted.idxstats:md5,39e30f2f398992208a5411c74a3c9774", + "Clone9_N2_mature.sorted.stats:md5,fb8c403012481dafb895013c555f6d85", + "Control_N2_mature.sorted.stats:md5,958b7a9ccfe3893b117317d00cd29949", + "Control_N3_mature.sorted.flagstat:md5,2831f55bccbcf666d1c313ef377bcb30", + true, + true, + true, + "Clone9_N3_mature.sorted.stats:md5,23b012dd60ea6dcec5cedb5a73ffc792", + true, + "Clone1_N3_mature.sorted.flagstat:md5,67fc6ba8516d4e5b3ed2a62febc92f0a", + "Clone9_N1_mature.sorted.idxstats:md5,4f5c53b3acc6ee228d5f5766bb4bf1d4", + true, + "Control_N1_mature.sorted.stats:md5,b4ffb3a7623e32420def4d3470a326ab", + "Control_N1_mature.sorted.idxstats:md5,ec6150327db493da8faaca1525afacd1", + "Clone9_N2_mature.sorted.flagstat:md5,247e02da50509fc1b3c5b35001922a8d", + "Control_N2_mature.sorted.flagstat:md5,cdeb62c8bd17760b6d258a17bec1e80c", + true, + true, + true, + true, + "Control_N2_mature.sorted.idxstats:md5,af6ecc38643b1aedf67354e91e95364e", + true, + "Clone9_N1_mature.sorted.flagstat:md5,014b846757652783ff3f954a966b8a1b", + true, + true, + "Clone9_N3_mature.sorted.idxstats:md5,84784ae05dce03ca691f7ae0b4074eb3", + true, + "Clone9_N2_mature.sorted.idxstats:md5,1ecdffcf833b08768c83bd74bf5e1a95", + true, + "Clone9_N3_mature.sorted.flagstat:md5,4f60cfd3527e91df204253f9f1aebfcd", + "Control_N3_mature.sorted.idxstats:md5,a38cb5edff03d442729ad3ab2dad5425", + true, + true, + true, + "Clone1_N1_mature.sorted.idxstats:md5,69adbd609e315faaa5b03082919c941f", + true, + "Clone1_N1_mature.sorted.flagstat:md5,f138a532bc7dab94f7cf4b4a4e5e23e5", + "Control_N3_mature.sorted.stats:md5,ff9dab4d3220aa44cdc80ea2fc311823", + true, + "Clone1_N3_mature.sorted.stats:md5,e8feced949af44c8e5d31523b12122b9", + true, + true, + true, + "Control_N1_mature.sorted.flagstat:md5,16318a574fe410b81c0e2cdf0dfa3c97", + "Clone9_N1_mature.sorted.stats:md5,02184884c17c8730f4df9e1a6144bbdc", + true, + true, + true, + true, + true, + true, + true, + true, + "mirna.tsv:md5,01179dda321cf235df8c1fb72609ecb4", + true, + true, + "mirtop_rawData.tsv:md5,98c46ade3ba0b141f1306c1dbc9a3ff1", + true, + "Clone1_N3.fastp_trimmed.fastq.gz:md5,2e395240c74b3870efe03dc329d8bad8", + "Control_N1.fastp_trimmed.fastq.gz:md5,2f09082eb68a8f1dc308050e330887ec", + "Control_N3.fastp_trimmed.fastq.gz:md5,342368a6e6acdaf0ae9379676b6d07f0", + "Clone9_N1.fastp_trimmed.fastq.gz:md5,115cf0c346a93a47ba782c5724b4f090", + "Clone1_N1.fastp_trimmed.fastq.gz:md5,14a2590e663dbde105780726c2173c25", + "Clone9_N2.fastp_trimmed.fastq.gz:md5,c922ec95a4b84d806dd2054ff0f9cab7", + "Clone9_N3.fastp_trimmed.fastq.gz:md5,67cf9a7d2fa431f0e772391ed1651f93", + "Control_N2.fastp_trimmed.fastq.gz:md5,d6e607edcb3d71c546ce8fdfb18e3999", + "hairpin.fa_igenome.fa_idx.fa:md5,f7ee61ca4537300386fdb85c7dec24d2", + "mature.fa_igenome.fa_idx.fa:md5,48215f56ca0bfbdbb1a28482457283e3", + "hairpin.fa_igenome.fa:md5,cddcc379892cb43e807ff54feafafbc1", + "mature.fa_igenome.fa:md5,48215f56ca0bfbdbb1a28482457283e3", + true, + true, + true, + true, + true, + true, + true, + true, + "hairpin_log2CPM_sample_distances.txt:md5,7cca5268281ff6e24f849526589b9e48", + true, + true, + true, + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T21:16:50.121115379" + } +} \ No newline at end of file diff --git a/tests/test_technical_repeats.nf.test b/tests/test_technical_repeats.nf.test index f01233aa..0d63faaa 100644 --- a/tests/test_technical_repeats.nf.test +++ b/tests/test_technical_repeats.nf.test @@ -18,7 +18,125 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 75 } + { assert workflow.trace.succeeded().size() == 75 }, + + { assert snapshot( + path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.edited.fa"), + path("$outputDir/bowtie_index/genome/genome.3.ebwt"), + path("$outputDir/bowtie_index/genome/genome.4.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") + ).match("bowtie_index") }, + + { assert snapshot( + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai").exists() + ).match("genome_quant") }, + + { assert snapshot( + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop.tsv").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop.gff").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists(), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists() + ).match("mirna_quant") }, + + { assert snapshot( + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") + ).match("mirtrace") }, + ) } diff --git a/tests/test_technical_repeats.nf.test.snap b/tests/test_technical_repeats.nf.test.snap new file mode 100644 index 00000000..47779b5a --- /dev/null +++ b/tests/test_technical_repeats.nf.test.snap @@ -0,0 +1,153 @@ +{ + "bowtie_index": { + "content": [ + "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", + "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", + "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", + "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", + "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", + "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", + "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", + "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", + "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", + "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", + "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", + "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", + "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", + "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", + "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", + "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", + "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", + "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", + "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T16:26:10.297696559" + }, + "mirtrace": { + "content": [ + "mirtrace-stats-rnatype.tsv:md5,2843855add34a73acd332a112bd80a34", + "mirtrace-stats-length.tsv:md5,71591c754eed9db419b91fb499f8e2ab", + "mirtrace-stats-contamination_detailed.tsv:md5,c16e27cc433dacdd5bfff09a9aaab736", + "mirtrace-stats-qcstatus.tsv:md5,37465e5d4d756792b95f187e6406fc6b", + "mirtrace-stats-contamination_basic.tsv:md5,ca3f99b1b89d2674864b62bbf9c41592", + "mirtrace-stats-phred.tsv:md5,1ac6fdae848cc4e39904edc361f75d1f", + "mirtrace-stats-mirna-complexity.tsv:md5,c69c4762a887a8e792c896dc5d3866b8", + "Clone1_N1.fastp.fasta:md5,7630d5d8f047d2f7e9492598e6f97c84", + "Control_N1.fastp.fasta:md5,534de89c8354a874458497804dcb7785", + "Clone9_N3.fastp.fasta:md5,0f2ef6c209a0b591d4eff5d77b713957", + "Clone1_N1.fastp.fasta:md5,f49d63f3d05aeb349f58f2bb95552332", + "Control_N1.fastp.fasta:md5,b34c20e0736351db5d0d1d3236de18ec", + "Clone9_N3.fastp.fasta:md5,726d1d14a88d7b816bb97bab9f006c45" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T16:26:13.960235236" + }, + "genome_quant": { + "content": [ + "Control_N1_mature_hairpin_genome.sorted.flagstat:md5,41e0b4dc62f9b8779534d67630ea6ab6", + "Clone9_N3_mature_hairpin_genome.sorted.stats:md5,872a90aca4d070f9403ae86b42666e2c", + "Clone9_N3_mature_hairpin_genome.sorted.flagstat:md5,50eb08817350b22dbe99bcc3dc7f2a38", + "Clone1_N1_mature_hairpin_genome.sorted.flagstat:md5,1d56901f0754350ee0925cff76bee6d1", + true, + true, + true, + "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,964b1ec118f45c5cb9443efc996b4b3e", + true, + "Control_N1_mature_hairpin_genome.sorted.idxstats:md5,6f43b2104f522103671ce78dc7d75b6d", + "Control_N1_mature_hairpin_genome.sorted.stats:md5,97f2c3ceb62b98d9169b226e954a1150", + true, + "Clone9_N3_mature_hairpin_genome.sorted.idxstats:md5,6561bdbc8589548d965823d7f43dee39", + "Clone1_N1_mature_hairpin_genome.sorted.idxstats:md5,f6408e25770f9a8530126900c314332f", + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T16:26:11.410550912" + }, + "software_versions": { + "content": [ + "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, CAT_FASTQ={cat=8.3}, FASTP={fastp=0.23.4}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_GENOME={bowtie=1.3.1}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T16:26:10.291195708" + }, + "mirna_quant": { + "content": [ + "Control_N1_mature_hairpin.sorted.stats:md5,41ed031d9ee3d775fab782beea7c2c5e", + "Control_N1_mature_hairpin.sorted.idxstats:md5,2bb41d5a20116c7457ef45c1b294d22d", + "Clone9_N3_mature_hairpin.sorted.flagstat:md5,79f3d50c45d9aa0d2525f5f1411e8dd5", + true, + "Control_N1_mature_hairpin.sorted.flagstat:md5,e727c4751070cf76ebfd484c0e37d990", + true, + "Clone1_N1_mature_hairpin.sorted.idxstats:md5,f2a16cf301d8cfd5f9f99edb610705c7", + "Clone9_N3_mature_hairpin.sorted.idxstats:md5,98db6ef38c05a65ee7ef5a7520f4f51c", + true, + true, + "Clone9_N3_mature_hairpin.sorted.stats:md5,52d607b29c6fae0a72cb55b83a5d550f", + "Clone1_N1_mature_hairpin.sorted.stats:md5,3fc6353abadc1c6e2687bc7a081f93a2", + true, + "Clone1_N1_mature_hairpin.sorted.flagstat:md5,f6d7848cf9c70cd3469ce1944d17be3c", + true, + true, + "Clone1_N1_mature.sorted.stats:md5,edfa6dab3271e66f743da2aca3ea7663", + true, + "Clone9_N3_mature.sorted.stats:md5,4fe47f64e7bdd0e1efeaa8271e92000a", + true, + true, + "Control_N1_mature.sorted.stats:md5,9abec7b88211f78d0e743dbedb1e1125", + "Control_N1_mature.sorted.idxstats:md5,8e96945e95b03c3c33867c98dece1e4e", + "Clone9_N3_mature.sorted.idxstats:md5,f92b6bdb8bf206757d8e2733f60f3c1b", + "Clone9_N3_mature.sorted.flagstat:md5,bbb6bc880f6fc9424fc16b095af752b9", + true, + true, + "Clone1_N1_mature.sorted.idxstats:md5,f80f8349d8a814e8f67ef4c30e2f6a53", + "Clone1_N1_mature.sorted.flagstat:md5,e6adf8d4926033f9ae6a0d5ab42bd267", + "Control_N1_mature.sorted.flagstat:md5,f10e74138d682fed95c076112b7f9236", + "mirna.tsv:md5,b884a1dadb2a803fc3838f124695c68c", + true, + true, + "mirtop_rawData.tsv:md5,edae282cde52e6b60d42962479866cb3", + true, + "Control_N1.fastp_trimmed.fastq.gz:md5,8d0676323aa9e84556cdf209db92b6ed", + "Clone1_N1.fastp_trimmed.fastq.gz:md5,1ce9b5ab0591aa067c0bcfbc4852cd19", + "Clone9_N3.fastp_trimmed.fastq.gz:md5,abb626ba9f41ef35a3684d2b5b4f2c4f", + "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", + "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", + "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + true, + true, + true, + true, + true, + true, + true, + true, + "hairpin_log2CPM_sample_distances.txt:md5,2d89f929eff72230c1a6e8bffc8fa17a", + true, + true, + true, + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T18:26:58.905465612" + } +} \ No newline at end of file diff --git a/tests/test_umi.nf.test b/tests/test_umi.nf.test index b905c55c..f7ea75cc 100644 --- a/tests/test_umi.nf.test +++ b/tests/test_umi.nf.test @@ -18,7 +18,171 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, - { assert workflow.trace.succeeded().size() == 64 } + { assert workflow.trace.succeeded().size() == 64 }, + + { assert snapshot( + path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.edited.fa"), + path("$outputDir/bowtie_index/genome/genome.3.ebwt"), + path("$outputDir/bowtie_index/genome/genome.4.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") + ).match("bowtie_index") }, + + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), + path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/mirtrace_contamination_check_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") + ).match("multiqc") }, + + { assert snapshot( + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats") + ).match("genome_quant") }, + + { assert snapshot( + path("$outputDir/umi_dedup/bam_deduplicated/SRX8195117_SRR11631013.umi_dedup.sorted.fastq.gz"), + path("$outputDir/umi_dedup/bam_deduplicated/SRX8195118_SRR11631014.umi_dedup.sorted.fastq.gz"), + path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195118_SRR11631014.umi_extract.fastq.gz"), + path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195117_SRR11631013.umi_extract.fastq.gz") + ).match("umi_dedup") }, + + { assert snapshot( + path("$outputDir/mirna_quant/bam/seqcluster/SRX8195117_SRR11631013_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/SRX8195118_SRR11631014_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195117_SRR11631013_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195118_SRR11631014_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/SRX8195118_SRR11631014_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/SRX8195117_SRR11631013_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195118_SRR11631014_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195117_SRR11631013_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop.tsv").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop.gff").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists(), + path("$outputDir/mirna_quant/seqcluster/final/SRX8195117_SRR11631013.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/SRX8195118_SRR11631014.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists() + ).match("mirna_quant") }, + + { assert snapshot( + path("$outputDir/fastqc/raw/SRX8195117_SRR11631013.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/SRX8195118_SRR11631014.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/SRX8195117_SRR11631013.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/SRX8195118_SRR11631014.trim_fastqc.zip").exists() + ).match("fastqc") }, + + { assert snapshot( + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/SRX8195118_SRR11631014.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/SRX8195117_SRR11631013.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/SRX8195118_SRR11631014.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/SRX8195117_SRR11631013.fastp.fasta") + ).match("mirtrace") }, + ) } diff --git a/tests/test_umi.nf.test.snap b/tests/test_umi.nf.test.snap new file mode 100644 index 00000000..0cdc75a2 --- /dev/null +++ b/tests/test_umi.nf.test.snap @@ -0,0 +1,217 @@ +{ + "bowtie_index": { + "content": [ + "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", + "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", + "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", + "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", + "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", + "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", + "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", + "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", + "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", + "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", + "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", + "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", + "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", + "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", + "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", + "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", + "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", + "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", + "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T16:41:27.150518197" + }, + "mirtrace": { + "content": [ + "mirtrace-stats-rnatype.tsv:md5,00e584439bec82f5de8d6485a73dec37", + "mirtrace-stats-length.tsv:md5,3edbc31452dba97f8b829e3f8f635955", + "mirtrace-stats-contamination_detailed.tsv:md5,428d2fd6ea0a6f2af1018a557e89bece", + "mirtrace-stats-qcstatus.tsv:md5,de4f8a670b736bedf348d358cfdfb9fc", + "mirtrace-stats-contamination_basic.tsv:md5,3d54b37ab3206e9fec909fe3ea1a4777", + "mirtrace-stats-phred.tsv:md5,8cf9fc2223b9aeb50f92c8845edbf535", + "mirtrace-stats-mirna-complexity.tsv:md5,cd2f37963adeee159764a89688a4a6a5", + "SRX8195118_SRR11631014.fastp.fasta:md5,99e2ce92ce102bd3fedc3a9d3b926873", + "SRX8195117_SRR11631013.fastp.fasta:md5,e0e31d882568a7853dea75b3c595108f", + "SRX8195118_SRR11631014.fastp.fasta:md5,7db07b8c0b9e2b484eb3d42a04e480d1", + "SRX8195117_SRR11631013.fastp.fasta:md5,eb1ba9fa6f7d956e5d650fdd306d5634" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T16:41:55.094313512" + }, + "umi_dedup": { + "content": [ + "SRX8195117_SRR11631013.umi_dedup.sorted.fastq.gz:md5,247d78a2d700012064d0b2e28d04b061", + "SRX8195118_SRR11631014.umi_dedup.sorted.fastq.gz:md5,af2b98d9bd6d0760a7eb07813d015aee", + "SRX8195118_SRR11631014.umi_extract.fastq.gz:md5,d2928324ae465d3d8eaf65c24418b8cf", + "SRX8195117_SRR11631013.umi_extract.fastq.gz:md5,1aeed318fab39fa646ff790a025bd21d" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T16:41:29.126845341" + }, + "genome_quant": { + "content": [ + true, + "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats:md5,a4874de294706a7ead30258944ff2dad", + true, + true, + "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats:md5,cc0413bf90252c3b3af8926fd64bc873", + "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat:md5,977e88cbe62027285df73e1f7f9cd9bc", + "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.flagstat:md5,235383f64a943885f5d899f5b8e03eba", + true, + "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats:md5,053912820064080299710bfbe7baf3c7", + "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats:md5,e19093f62044a7d053a0073092c506f3" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T21:46:41.554061063" + }, + "software_versions": { + "content": [ + "{BOWTIE_MAP_GENOME={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTP={fastp=0.23.4}, FASTP_LENGTH_FILTER={fastp=0.23.4}, FASTQC_RAW={fastqc=0.12.1}, FASTQC_TRIM={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_GENOME={bowtie=1.3.1}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, UMICOLLAPSE_FASTQ={umicollapse=1.0.0-1}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T16:41:27.144202619" + }, + "fastqc": { + "content": [ + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T21:46:44.744398069" + }, + "multiqc": { + "content": [ + "fastqc-status-check-heatmap.txt:md5,c1509fdd74b21a718fe099de64514995", + "fastp_filtered_reads_plot.txt:md5,3aaa79e1ede44347971c26100d9e954b", + true, + "fastqc_sequence_counts_plot-1.txt:md5,24744e039ce4dbcbacf42edbfd642a8b", + "mirtrace_complexity_plot.txt:md5,5a860a872f793250b8c4482d031176a8", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,351f949c0abf4fb7587f3f5d9a28d461", + "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", + "samtools-stats-dp.txt:md5,74808822577fb62efb39811272e6919e", + "fastqc_sequence_length_distribution_plot.txt:md5,8c34b57ec084e2da9d62c254c0a517f4", + "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,dfdb23f41359b8a6b84d6626a0474d02", + "fastqc_sequence_duplication_levels_plot-1.txt:md5,b5ae95ecd73055798ed70947dda3747c", + "fastqc_per_base_sequence_quality_plot-1.txt:md5,89adfa92b1cde0ad4e401b430bbc68ce", + true, + "fastqc_per_base_n_content_plot-1.txt:md5,db081d3aa63007e5a78113f0fc26f27d", + "fastqc_per_base_n_content_plot.txt:md5,5b5b8cee3162d092c0bcddffbd000f34", + "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,66a47c7ce00ede2053f8e6eb20ec3417", + "fastqc_per_sequence_quality_scores_plot.txt:md5,3aa99649540afc898d32d2e49a364487", + "mirtrace_qc_plot.txt:md5,b08d11ea51c54e615f9608002644c787", + "fastqc_per_sequence_quality_scores_plot-1.txt:md5,4108da6fe352558a652ee2b17d609e07", + "mirtrace_length_plot.txt:md5,440a84ce9bbdb89b736e4e2446382665", + true, + "fastqc-status-check-heatmap-1.txt:md5,cb2ea844834808ae4c95c6440269cf2e", + "fastqc_sequence_counts_plot.txt:md5,5e5c5132ff1969dfa40cb8b1eadf7a46", + "mirtrace_rna_categories_plot.txt:md5,6d08c297377a6241c4c1e82278d71f32", + "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,f36b7cfd3057b26281367397db45033a", + "samtools_alignment_plot.txt:md5,5e828961dbd55a6d6872221c49dfdc59", + "fastqc_per_base_sequence_quality_plot.txt:md5,e2e187bc0b0c1f0d1abb3b666945c7b3", + true, + "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,bbad2035ada86867c4ed579a93b78d64", + true, + true, + "mirtrace_contamination_check_plot.txt:md5,7f12917ce506127a729edb733fdda511", + "fastqc_adapter_content_plot.txt:md5,de1d7324ff5146b49fc9a2e6d4633962", + "fastqc_sequence_duplication_levels_plot.txt:md5,fe7598e49f93bb980a7675a2bb4bd3b5", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,c2f2f9282a50c3eef475664cc969b8ec", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,15d8fa32e0c11ef0d3d10fc28370972c", + "fastqc_adapter_content_plot-1.txt:md5,89cd342fdc6fbba5f67078c9a2f0c684", + "fastp-seq-content-gc-plot_Read_1_Before_filtering.txt:md5,f832e92fb36db181ed1079be110edb2a", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,488e25de89d18d20f29b86f2580a8df9", + true, + "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,d673e3b18c40c5af1edccffba386d678" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T16:41:28.310980133" + }, + "mirna_quant": { + "content": [ + true, + true, + true, + true, + "SRX8195117_SRR11631013_mature_hairpin.sorted.idxstats:md5,4e7c1c98804febf6210cee5e3941709e", + "SRX8195118_SRR11631014_mature_hairpin.sorted.flagstat:md5,e0c44533bc7813d552de4864d997c916", + "SRX8195118_SRR11631014_mature_hairpin.sorted.idxstats:md5,f4485713620f31d97a5006acdf6d8a5d", + "SRX8195117_SRR11631013_mature_hairpin.sorted.stats:md5,b3ff5680bfebaaf6e30bb43a29a3031c", + "SRX8195117_SRR11631013_mature_hairpin.sorted.flagstat:md5,b86bd14dc687a26ba5a84d1015f4b70a", + true, + true, + true, + true, + true, + "SRX8195118_SRR11631014_mature_hairpin.sorted.stats:md5,da76c29d304c53210242909c3e23a29a", + true, + true, + true, + true, + "SRX8195118_SRR11631014_mature.sorted.idxstats:md5,8b9cf0f1647b938f058b80522df24667", + true, + true, + "SRX8195117_SRR11631013_mature.sorted.flagstat:md5,171387fb18ba9868e28ca03d24a7daca", + "SRX8195118_SRR11631014_mature.sorted.stats:md5,bf67cbae75e68e5de07d042487010498", + "SRX8195118_SRR11631014_mature.sorted.flagstat:md5,57c6d477394d367ebae59f7267b430a5", + "SRX8195117_SRR11631013_mature.sorted.stats:md5,c5ed9f69f29172af201968f97b49be67", + true, + "SRX8195117_SRR11631013_mature.sorted.idxstats:md5,fb6c4000f82a66654b4f2a40570649b5", + true, + true, + true, + true, + "mirna.tsv:md5,e30f3037522a0a20f2a4b32cbb70990a", + true, + true, + "mirtop_rawData.tsv:md5,ed4a0ceb2e8cd1721aa5ed27270f9623", + true, + "SRX8195117_SRR11631013.fastp_trimmed.fastq.gz:md5,0a0da4dc5c49678d8421537dbf3067bc", + "SRX8195118_SRR11631014.fastp_trimmed.fastq.gz:md5,cf4de7d3978d5ff4709a88d3d2d034d8", + "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", + "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", + "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + true, + true, + true, + true, + true, + true, + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-21T21:46:44.500946722" + } +} \ No newline at end of file From fd3405d4a2f8b468df14dda9fb33be63c88d12f3 Mon Sep 17 00:00:00 2001 From: zxBIB Schcolnicov Date: Thu, 22 Aug 2024 15:27:08 +0200 Subject: [PATCH 06/15] Updated tests and snaps --- tests/test.nf.test | 6 +++--- tests/test.nf.test.snap | 10 +++++----- tests/test_index.nf.test | 6 +++--- tests/test_index.nf.test.snap | 10 +++++----- tests/test_mirgenedb.nf.test | 6 +++--- tests/test_mirgenedb.nf.test.snap | 10 +++++----- tests/test_no_genome.nf.test | 6 +++--- tests/test_no_genome.nf.test.snap | 10 +++++----- tests/test_technical_repeats.nf.test | 2 +- tests/test_technical_repeats.nf.test.snap | 4 ++-- tests/test_umi.nf.test | 4 ++-- tests/test_umi.nf.test.snap | 6 +++--- 12 files changed, 40 insertions(+), 40 deletions(-) diff --git a/tests/test.nf.test b/tests/test.nf.test index e161bbfa..e70b30e0 100644 --- a/tests/test.nf.test +++ b/tests/test.nf.test @@ -51,7 +51,7 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), @@ -70,7 +70,7 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), @@ -236,7 +236,7 @@ nextflow_pipeline { path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap index d7f9fc23..3f49d724 100644 --- a/tests/test.nf.test.snap +++ b/tests/test.nf.test.snap @@ -153,7 +153,7 @@ "mirtrace_complexity_plot.txt:md5,5f78d6f559a9642e68e1fd74ac2c11ca", "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", - "samtools-stats-dp.txt:md5,61a77aab820a3eba21a51e32168b45e3", + true, "fastqc_sequence_length_distribution_plot.txt:md5,13f72b3be854c74cd7b5176ca0583770", "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", "fastqc_sequence_duplication_levels_plot-1.txt:md5,06a4162d4787883b1f39a1b9acb7bb91", @@ -172,7 +172,7 @@ "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", "mirtrace_rna_categories_plot.txt:md5,8665376e2a123e1661f82cbbee54789f", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", - "samtools_alignment_plot.txt:md5,f87f3d2101f70e840c57df850bd1e3be", + true, "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", true, "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", @@ -192,7 +192,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-20T19:07:57.481787644" + "timestamp": "2024-08-22T13:46:26.862902905" }, "mirna_quant": { "content": [ @@ -301,7 +301,7 @@ true, true, true, - "hairpin_log2CPM_sample_distances.txt:md5,b19fa1d9f821fc8e2c0e9f34f76b5479", + true, true, true, true, @@ -314,6 +314,6 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-21T17:33:19.815567664" + "timestamp": "2024-08-22T13:46:30.62317228" } } \ No newline at end of file diff --git a/tests/test_index.nf.test b/tests/test_index.nf.test index ce38dbdf..36a67a41 100644 --- a/tests/test_index.nf.test +++ b/tests/test_index.nf.test @@ -44,7 +44,7 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), @@ -63,7 +63,7 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), @@ -203,7 +203,7 @@ nextflow_pipeline { path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), diff --git a/tests/test_index.nf.test.snap b/tests/test_index.nf.test.snap index 3169c975..78238110 100644 --- a/tests/test_index.nf.test.snap +++ b/tests/test_index.nf.test.snap @@ -126,7 +126,7 @@ "mirtrace_complexity_plot.txt:md5,5f78d6f559a9642e68e1fd74ac2c11ca", "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", - "samtools-stats-dp.txt:md5,0f88cdcc523ea239c2dd7e1e2decec36", + true, "fastqc_sequence_length_distribution_plot.txt:md5,13f72b3be854c74cd7b5176ca0583770", "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", "fastqc_sequence_duplication_levels_plot-1.txt:md5,06a4162d4787883b1f39a1b9acb7bb91", @@ -145,7 +145,7 @@ "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", "mirtrace_rna_categories_plot.txt:md5,8665376e2a123e1661f82cbbee54789f", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", - "samtools_alignment_plot.txt:md5,ac24d7f3bf5858e7550d2f93446137e1", + true, "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", true, "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", @@ -165,7 +165,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-20T20:50:18.947900403" + "timestamp": "2024-08-22T13:59:07.022344773" }, "mirna_quant": { "content": [ @@ -274,7 +274,7 @@ true, true, true, - "hairpin_log2CPM_sample_distances.txt:md5,b19fa1d9f821fc8e2c0e9f34f76b5479", + true, true, true, true, @@ -287,6 +287,6 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-21T17:43:32.069747201" + "timestamp": "2024-08-22T13:59:15.6558314" } } \ No newline at end of file diff --git a/tests/test_mirgenedb.nf.test b/tests/test_mirgenedb.nf.test index 6a4f243e..1b594f7f 100644 --- a/tests/test_mirgenedb.nf.test +++ b/tests/test_mirgenedb.nf.test @@ -116,7 +116,7 @@ nextflow_pipeline { path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), @@ -224,7 +224,7 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), @@ -239,7 +239,7 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt").exists(), path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), diff --git a/tests/test_mirgenedb.nf.test.snap b/tests/test_mirgenedb.nf.test.snap index 375fabc4..8aee6b90 100644 --- a/tests/test_mirgenedb.nf.test.snap +++ b/tests/test_mirgenedb.nf.test.snap @@ -120,7 +120,7 @@ "fastqc_sequence_counts_plot-1.txt:md5,37d8ae6c5734eb2679e65e46c9af9101", "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", "multiqc_citations.txt:md5,57db2426be011862828d18f767d25b57", - "samtools-stats-dp.txt:md5,90d663100472e8b52c2c04c9ee28babf", + true, "fastqc_sequence_length_distribution_plot.txt:md5,13f72b3be854c74cd7b5176ca0583770", "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", "fastqc_sequence_duplication_levels_plot-1.txt:md5,06a4162d4787883b1f39a1b9acb7bb91", @@ -135,7 +135,7 @@ "fastqc_overrepresented_sequences_plot-1.txt:md5,1de000de50cc7516bb9d996def14c6eb", "fastqc-status-check-heatmap-1.txt:md5,e64c353797e6dc057d10b3194ca6b20d", "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", - "samtools_alignment_plot.txt:md5,07766860ac4d8739fcec6b5b51289b57", + true, true, "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", @@ -153,7 +153,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-21T17:57:21.712642814" + "timestamp": "2024-08-22T14:16:09.201918482" }, "mirna_quant": { "content": [ @@ -251,7 +251,7 @@ "Control_N2_mature_hairpin.sorted.flagstat:md5,c830a70e5badf24c4c2067d5d856853e", true, true, - "hairpin_log2CPM_sample_distances.txt:md5,ee28abcd0c9c3c05d22453e1039fe6a1", + true, true, true, true, @@ -270,6 +270,6 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-21T17:57:09.190802792" + "timestamp": "2024-08-22T14:16:03.791070797" } } \ No newline at end of file diff --git a/tests/test_no_genome.nf.test b/tests/test_no_genome.nf.test index bd38e938..eae840db 100644 --- a/tests/test_no_genome.nf.test +++ b/tests/test_no_genome.nf.test @@ -44,7 +44,7 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), @@ -63,7 +63,7 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), @@ -234,7 +234,7 @@ nextflow_pipeline { path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), diff --git a/tests/test_no_genome.nf.test.snap b/tests/test_no_genome.nf.test.snap index 6522d674..f148ab9e 100644 --- a/tests/test_no_genome.nf.test.snap +++ b/tests/test_no_genome.nf.test.snap @@ -97,7 +97,7 @@ "mirtrace_complexity_plot.txt:md5,5f78d6f559a9642e68e1fd74ac2c11ca", "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", - "samtools-stats-dp.txt:md5,951e248c4dce68d25e14f0c79ef36e2e", + true, "fastqc_sequence_length_distribution_plot.txt:md5,13f72b3be854c74cd7b5176ca0583770", "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", "fastqc_sequence_duplication_levels_plot-1.txt:md5,06a4162d4787883b1f39a1b9acb7bb91", @@ -116,7 +116,7 @@ "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", "mirtrace_rna_categories_plot.txt:md5,8665376e2a123e1661f82cbbee54789f", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", - "samtools_alignment_plot.txt:md5,e4335c4194bffb41df16619f3abfe705", + true, "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", true, "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,048e9b2293217ab8b47ba0113b83c76c", @@ -136,7 +136,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-21T16:07:41.27780496" + "timestamp": "2024-08-22T14:27:56.186904169" }, "mirna_quant": { "content": [ @@ -293,7 +293,7 @@ true, true, true, - "hairpin_log2CPM_sample_distances.txt:md5,7cca5268281ff6e24f849526589b9e48", + true, true, true, true, @@ -306,6 +306,6 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-21T21:16:50.121115379" + "timestamp": "2024-08-22T14:28:01.247994982" } } \ No newline at end of file diff --git a/tests/test_technical_repeats.nf.test b/tests/test_technical_repeats.nf.test index 0d63faaa..1325e605 100644 --- a/tests/test_technical_repeats.nf.test +++ b/tests/test_technical_repeats.nf.test @@ -111,7 +111,7 @@ nextflow_pipeline { path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt"), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), diff --git a/tests/test_technical_repeats.nf.test.snap b/tests/test_technical_repeats.nf.test.snap index 47779b5a..6c3cbcd2 100644 --- a/tests/test_technical_repeats.nf.test.snap +++ b/tests/test_technical_repeats.nf.test.snap @@ -135,7 +135,7 @@ true, true, true, - "hairpin_log2CPM_sample_distances.txt:md5,2d89f929eff72230c1a6e8bffc8fa17a", + true, true, true, true, @@ -148,6 +148,6 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-21T18:26:58.905465612" + "timestamp": "2024-08-22T14:44:11.679737041" } } \ No newline at end of file diff --git a/tests/test_umi.nf.test b/tests/test_umi.nf.test index f7ea75cc..e3ba0b12 100644 --- a/tests/test_umi.nf.test +++ b/tests/test_umi.nf.test @@ -50,7 +50,7 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), @@ -68,7 +68,7 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), diff --git a/tests/test_umi.nf.test.snap b/tests/test_umi.nf.test.snap index 0cdc75a2..de8febc7 100644 --- a/tests/test_umi.nf.test.snap +++ b/tests/test_umi.nf.test.snap @@ -111,7 +111,7 @@ "mirtrace_complexity_plot.txt:md5,5a860a872f793250b8c4482d031176a8", "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,351f949c0abf4fb7587f3f5d9a28d461", "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", - "samtools-stats-dp.txt:md5,74808822577fb62efb39811272e6919e", + true, "fastqc_sequence_length_distribution_plot.txt:md5,8c34b57ec084e2da9d62c254c0a517f4", "fastp-seq-content-n-plot_Read_1_Before_filtering.txt:md5,dfdb23f41359b8a6b84d6626a0474d02", "fastqc_sequence_duplication_levels_plot-1.txt:md5,b5ae95ecd73055798ed70947dda3747c", @@ -129,7 +129,7 @@ "fastqc_sequence_counts_plot.txt:md5,5e5c5132ff1969dfa40cb8b1eadf7a46", "mirtrace_rna_categories_plot.txt:md5,6d08c297377a6241c4c1e82278d71f32", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,f36b7cfd3057b26281367397db45033a", - "samtools_alignment_plot.txt:md5,5e828961dbd55a6d6872221c49dfdc59", + true, "fastqc_per_base_sequence_quality_plot.txt:md5,e2e187bc0b0c1f0d1abb3b666945c7b3", true, "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,bbad2035ada86867c4ed579a93b78d64", @@ -150,7 +150,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-21T16:41:28.310980133" + "timestamp": "2024-08-22T15:03:17.200671813" }, "mirna_quant": { "content": [ From b598f731ae24a69ac9bb404c308967be82b77054 Mon Sep 17 00:00:00 2001 From: zxBIB Schcolnicov Date: Thu, 22 Aug 2024 19:17:31 +0200 Subject: [PATCH 07/15] Updated test_index test --- tests/test_index.nf.test | 392 +++++++++++++++++---------------- tests/test_index.nf.test.snap | 394 ++++++++++++++++++++-------------- 2 files changed, 441 insertions(+), 345 deletions(-) diff --git a/tests/test_index.nf.test b/tests/test_index.nf.test index 36a67a41..311277a6 100644 --- a/tests/test_index.nf.test +++ b/tests/test_index.nf.test @@ -21,225 +21,175 @@ nextflow_pipeline { { assert workflow.trace.succeeded().size() == 161 }, { assert snapshot( - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, - - { assert snapshot( - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt").exists(), - path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") - ).match("multiqc") }, - - { assert snapshot( - path("$outputDir/untar/bowtie_index/genome.rev.2.ebwt"), - path("$outputDir/untar/bowtie_index/genome.2.ebwt"), path("$outputDir/untar/bowtie_index/genome.1.ebwt"), path("$outputDir/untar/bowtie_index/genome.3.ebwt"), + path("$outputDir/untar/bowtie_index/genome.2.ebwt"), + path("$outputDir/untar/bowtie_index/genome.rev.1.ebwt"), path("$outputDir/untar/bowtie_index/genome.4.ebwt"), - path("$outputDir/untar/bowtie_index/genome.rev.1.ebwt") - ).match("untar") }, + path("$outputDir/untar/bowtie_index/genome.rev.2.ebwt") + ).match("untar_bowtie_index") }, { assert snapshot( - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists() - ).match("genome_quant") }, + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa") + ).match("mirna_quant_reference") }, { assert snapshot( - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz") + ).match("mirna_quant_seqcluster") }, + + { assert snapshot( + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats") + ).match("mirna_quant_bam") }, + + { assert snapshot( + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), path("$outputDir/mirna_quant/mirtop/mirtop.tsv").exists(), path("$outputDir/mirna_quant/mirtop/mirtop.gff").exists(), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists(), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists() + ).match("mirna_quant_mirtop") }, + + { assert snapshot( + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists() - ).match("mirna_quant") }, + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists() + ).match("mirna_quant_edger_qc") }, { assert snapshot( + path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip").exists() + ).match("fastqc_raw") }, + + { assert snapshot( path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip").exists(), path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip").exists() - ).match("fastqc") }, + path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip").exists() + ).match("fastqc_trimmed") }, { assert snapshot( path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv") + ).match("mirtrace") }, + + { assert snapshot( path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), @@ -247,7 +197,10 @@ nextflow_pipeline { path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta") + ).match("mirtrace_qc_passed_reads.all.collapsed") }, + + { assert snapshot( path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), @@ -256,7 +209,78 @@ nextflow_pipeline { path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") - ).match("mirtrace") }, + ).match("mirtrace_qc_passed_reads.rnatype_unknown.collapsed") }, + + { assert snapshot( + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt") + ).match("bowtie_index_mirna_mature") }, + + { assert snapshot( + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt") + ).match("bowtie_index_mirna_hairpin") }, + + { assert snapshot( + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats") + ).match("genome_quant_bam") }, + + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), + path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") + ).match("multiqc_multiqc_data") }, ) } diff --git a/tests/test_index.nf.test.snap b/tests/test_index.nf.test.snap index 78238110..3cb0d6ba 100644 --- a/tests/test_index.nf.test.snap +++ b/tests/test_index.nf.test.snap @@ -1,70 +1,49 @@ { - "bowtie_index": { + "fastqc_trimmed": { "content": [ - "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", - "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", - "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", - "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", - "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", - "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", - "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", - "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", - "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", - "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", - "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", - "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" + true, + true, + true, + true, + true, + true, + true, + true ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-20T20:50:18.193559565" + "timestamp": "2024-08-22T19:07:36.900487683" }, "mirtrace": { "content": [ "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", - "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", - "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", + "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", - "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638", - "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", - "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", - "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", - "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", - "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", - "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", - "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", - "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8", - "Clone1_N1.fastp.fasta:md5,e297dfa46353946d6c140e4513dd4525", - "Clone9_N1.fastp.fasta:md5,63a17d136548fc98f34c8d98006cc7da", - "Control_N3.fastp.fasta:md5,d9980a598ece252e19d6c9ebefd51861", - "Control_N1.fastp.fasta:md5,e964e05ce2c93937a8e76602f2e08150", - "Clone9_N2.fastp.fasta:md5,b1ca39e6e1e75ee7d654d9ccfb35e906", - "Control_N2.fastp.fasta:md5,8cefbc494be7b363b19c10b8c00366b2", - "Clone1_N3.fastp.fasta:md5,4012282462dde0750f09cec883304cc3", - "Clone9_N3.fastp.fasta:md5,f733e20eb8d2a2009ca82464e8ccb148" + "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", + "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638" ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-20T20:50:30.083738998" + "timestamp": "2024-08-22T19:07:50.05985187" }, - "genome_quant": { + "mirna_quant_reference": { "content": [ - "Control_N2_mature_hairpin_genome.sorted.flagstat:md5,b0d42e94b2e0e026cd32a88dce40722c", - "Control_N2_mature_hairpin_genome.sorted.stats:md5,1222b755feaf406ecea3f2abb35a737c", - "Control_N2_mature_hairpin_genome.sorted.idxstats:md5,b6da32ce230fdeab39f3c4d5dcf41a3a", - true, - true + "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", + "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77" ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-20T20:50:19.817165699" + "timestamp": "2024-08-22T19:06:50.940201041" }, "software_versions": { "content": [ @@ -74,9 +53,98 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-20T20:50:18.088216994" + "timestamp": "2024-08-22T19:06:50.443184087" + }, + "mirna_quant_bam": { + "content": [ + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + true, + "Control_N1_mature.sorted.flagstat:md5,16318a574fe410b81c0e2cdf0dfa3c97", + "Clone1_N3_mature.sorted.flagstat:md5,67fc6ba8516d4e5b3ed2a62febc92f0a", + "Clone9_N3_mature.sorted.flagstat:md5,4f60cfd3527e91df204253f9f1aebfcd", + "Clone9_N2_mature.sorted.flagstat:md5,247e02da50509fc1b3c5b35001922a8d", + "Clone1_N1_mature.sorted.idxstats:md5,77ed64ddd23cf07340b65c04559d4726", + "Clone9_N2_mature.sorted.idxstats:md5,c9643d610de2f4d449a876e41dcab872", + "Control_N1_mature.sorted.stats:md5,b4ffb3a7623e32420def4d3470a326ab", + "Clone9_N3_mature.sorted.idxstats:md5,dee54e8e22dfca24acc290bf89a05cd4", + "Control_N1_mature.sorted.idxstats:md5,847bc5c6ef44e1f9754e47e648a5ef98", + "Clone1_N3_mature.sorted.stats:md5,e8feced949af44c8e5d31523b12122b9", + "Clone9_N3_mature.sorted.stats:md5,23b012dd60ea6dcec5cedb5a73ffc792", + "Control_N3_mature.sorted.flagstat:md5,2831f55bccbcf666d1c313ef377bcb30", + 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"Control_N1.fastp.fasta:md5,e964e05ce2c93937a8e76602f2e08150", + "Clone9_N2.fastp.fasta:md5,b1ca39e6e1e75ee7d654d9ccfb35e906", + "Control_N2.fastp.fasta:md5,8cefbc494be7b363b19c10b8c00366b2", + "Clone1_N3.fastp.fasta:md5,4012282462dde0750f09cec883304cc3", + "Clone9_N3.fastp.fasta:md5,f733e20eb8d2a2009ca82464e8ccb148" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T19:08:39.709442943" + }, + "genome_quant_bam": { + "content": [ true, true, + "Control_N2_mature_hairpin_genome.sorted.flagstat:md5,b0d42e94b2e0e026cd32a88dce40722c", + "Control_N2_mature_hairpin_genome.sorted.idxstats:md5,b6da32ce230fdeab39f3c4d5dcf41a3a", + "Control_N2_mature_hairpin_genome.sorted.stats:md5,1222b755feaf406ecea3f2abb35a737c" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T19:09:49.007300611" + }, + "bowtie_index_mirna_mature": { + "content": [ + "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", + "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", + "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", + "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f", + "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", + "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T19:09:14.547618596" + }, + "bowtie_index_mirna_hairpin": { + "content": [ + "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", + "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", + "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", + "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", + "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", + "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T19:09:27.72464599" + }, + "mirtrace_qc_passed_reads.all.collapsed": { + "content": [ + "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", + "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", + "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", + "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", + "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", + "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", + "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", + "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T19:07:59.93600436" + }, + "mirna_quant_mirtop": { + "content": [ + "mirtop_rawData.tsv:md5,774410dd2cf1e5be83bf8d6e1e8b96b0", true, true, + "mirna.tsv:md5,1f840afe7ab68eac73feaaad321b64f6", true ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T13:59:15.6558314" + "timestamp": "2024-08-22T19:07:04.940104262" } } \ No newline at end of file From 0f8ab7fe89f18334543f85ab6666895ae1995225 Mon Sep 17 00:00:00 2001 From: zxBIB Schcolnicov Date: Thu, 22 Aug 2024 21:59:27 +0200 Subject: [PATCH 08/15] Updated tests to split snapshot by subdirectories --- tests/test.nf.test | 454 ++++++++++++++------------- tests/test_index.nf.test | 2 +- tests/test_mirgenedb.nf.test | 238 +++++++------- tests/test_no_genome.nf.test | 439 ++++++++++++++------------ tests/test_technical_repeats.nf.test | 189 ++++++----- tests/test_umi.nf.test | 251 ++++++++------- 6 files changed, 850 insertions(+), 723 deletions(-) diff --git a/tests/test.nf.test b/tests/test.nf.test index e70b30e0..cbe3a64c 100644 --- a/tests/test.nf.test +++ b/tests/test.nf.test @@ -1,3 +1,4 @@ + nextflow_pipeline { name "Test Workflow main.nf - test" @@ -21,258 +22,194 @@ nextflow_pipeline { { assert workflow.trace.succeeded().size() == 196 }, { assert snapshot( - path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), path("$outputDir/bowtie_index/genome/genome.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.edited.fa"), path("$outputDir/bowtie_index/genome/genome.3.ebwt"), + path("$outputDir/bowtie_index/genome/genome.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), path("$outputDir/bowtie_index/genome/genome.4.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.edited.fa"), + path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt") + ).match("bowtie_index_genome") }, + + { assert snapshot( path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt") + ).match("bowtie_index_mirna_mature") }, { assert snapshot( - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt").exists(), - path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") - ).match("multiqc") }, + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt") + ).match("bowtie_index_mirna_hairpin") }, { assert snapshot( - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai").exists() - ).match("genome_quant") }, + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa") + ).match("mirna_quant_reference") }, { assert snapshot( - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz") + ).match("mirna_quant_seqcluster") }, + + { assert snapshot( + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat") + ).match("mirna_quant_bam") }, + + { assert snapshot( + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), path("$outputDir/mirna_quant/mirtop/mirtop.tsv").exists(), path("$outputDir/mirna_quant/mirtop/mirtop.gff").exists(), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists(), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists() + ).match("mirna_quant_mirtop") }, + + { assert snapshot( + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists() - ).match("mirna_quant") }, + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists() + ).match("mirna_quant_edger_qc") }, { assert snapshot( - path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip").exists() + ).match("fastqc_raw") }, + + { assert snapshot( path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip").exists(), path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip").exists() - ).match("fastqc") }, + path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip").exists() + ).match("fastqc_trimmed") }, { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv") + ).match("mirtrace") }, + + { assert snapshot( path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), @@ -280,7 +217,10 @@ nextflow_pipeline { path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta") + ).match("mirtrace_qc_passed_reads.all.collapsed") }, + + { assert snapshot( path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), @@ -289,7 +229,95 @@ nextflow_pipeline { path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") - ).match("mirtrace") }, + ).match("mirtrace_qc_passed_reads.rnatype_unknown.collapsed") }, + + { assert snapshot( + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat") + ).match("genome_quant_bam") }, + + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), + path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") + ).match("multiqc_multiqc_data") }, ) } diff --git a/tests/test_index.nf.test b/tests/test_index.nf.test index 311277a6..481d56e1 100644 --- a/tests/test_index.nf.test +++ b/tests/test_index.nf.test @@ -232,7 +232,7 @@ nextflow_pipeline { { assert snapshot( path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists(), path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), + //path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), //this file is outputed by the profile but it is not outputed while running CI tests path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats") ).match("genome_quant_bam") }, diff --git a/tests/test_mirgenedb.nf.test b/tests/test_mirgenedb.nf.test index 1b594f7f..c9051838 100644 --- a/tests/test_mirgenedb.nf.test +++ b/tests/test_mirgenedb.nf.test @@ -21,11 +21,42 @@ nextflow_pipeline { { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, { assert workflow.trace.succeeded().size() == 193 }, + { assert snapshot( + path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.3.ebwt"), + path("$outputDir/bowtie_index/genome/genome.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.4.ebwt"), + path("$outputDir/bowtie_index/genome/genome.edited.fa"), + path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt") + ).match("bowtie_index_genome") }, + + { assert snapshot( + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt") + ).match("bowtie_index_mirna_hairpin") }, + + { assert snapshot( + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt") + ).match("bowtie_index_mirna_mature") }, + { assert snapshot( path("$outputDir/mirna_quant/reference/hsa-hg38-pri-30-30.fas_igenome.fa"), path("$outputDir/mirna_quant/reference/hsa_igenome.fa"), path("$outputDir/mirna_quant/reference/hsa-hg38-pri-30-30.fas_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hsa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hsa_igenome.fa_idx.fa") + ).match("mirna_quant_reference") }, + + { assert snapshot( path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), @@ -33,188 +64,175 @@ nextflow_pipeline { path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz") + ).match("mirna_quant_seqcluster") }, + + { assert snapshot( path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats") + ).match("mirna_quant_bam") }, + + { assert snapshot( path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists() - ).match("mirna_quant") }, - - { assert snapshot( - path("$outputDir/bowtie_index/genome/genome.3.ebwt"), - path("$outputDir/bowtie_index/genome/genome.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.4.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.edited.fa"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt") - ).match("bowtie_index") }, + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists() + ).match("mirna_quant_edger_qc") }, { assert snapshot( path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip").exists() + ).match("fastqc_raw") }, + + { assert snapshot( path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip").exists(), path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip").exists(), path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip").exists(), path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip").exists() - ).match("fastqc") }, + path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip").exists() + ).match("fastqc_trimmed") }, { assert snapshot( path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam").exists(), path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam").exists(), path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.bam.bai").exists(), path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam").exists(), path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.bam.bai").exists(), path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.bai").exists(), path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.bam.bai").exists(), path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.flagstat"), path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.idxstats"), path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.flagstat"), path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N2_mature_hairpin_genome.sorted.stats"), path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N3_mature_hairpin_genome.sorted.stats") - ).match("genome_quant") }, + path("$outputDir/genome_quant/bam/Clone1_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats") + ).match("genome_quant_bam") }, { assert snapshot( path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), @@ -237,11 +255,11 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt").exists(), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), @@ -252,7 +270,7 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") - ).match("multiqc") }, + ).match("multiqc_multiqc_data") }, ) } diff --git a/tests/test_no_genome.nf.test b/tests/test_no_genome.nf.test index eae840db..2f60b070 100644 --- a/tests/test_no_genome.nf.test +++ b/tests/test_no_genome.nf.test @@ -1,3 +1,4 @@ + nextflow_pipeline { name "Test Workflow main.nf - test_no_genome" @@ -21,256 +22,214 @@ nextflow_pipeline { { assert workflow.trace.succeeded().size() == 147 }, { assert snapshot( - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa") + ).match("mirna_quant_reference") }, { assert snapshot( - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), - path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), - path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt").exists(), - path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), - path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), - path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") - ).match("multiqc") }, + path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz") + ).match("mirna_quant_seqcluster") }, { assert snapshot( - path("$outputDir/mirna_quant/bam/seqcluster/Control_N3_seqcluster.bam").exists(), path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N3_seqcluster.bam").exists(), - path("$outputDir/mirna_quant/bam/seqcluster/Control_N1_seqcluster.bam").exists(), - path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N2_seqcluster.bam").exists(), - path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N3_seqcluster.bam").exists(), - path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N1_seqcluster.bam").exists(), path("$outputDir/mirna_quant/bam/seqcluster/Control_N2_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N3_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N2_seqcluster.bam").exists(), path("$outputDir/mirna_quant/bam/seqcluster/Clone9_N1_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/Control_N1_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/Clone1_N1_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/Control_N3_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N3_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N2_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N3_seqcluster_unmapped.fq.gz").exists(), path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N2_seqcluster_unmapped.fq.gz").exists(), path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N1_seqcluster_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N1_seqcluster_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N3_seqcluster_unmapped.fq.gz").exists(), path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N1_seqcluster_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone9_N3_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Clone1_N1_seqcluster_unmapped.fq.gz").exists(), path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N3_seqcluster_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/Control_N2_seqcluster_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N1_mature_hairpin_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N1_mature_hairpin_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N3_mature_hairpin_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N2_mature_hairpin_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N2_mature_hairpin_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N3_mature_hairpin_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N3_mature_hairpin_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N1_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N2_mature.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N3_mature_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N1_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N2_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Control_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N2_mature_unmapped.fq.gz").exists(), path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N3_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone1_N3_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N1_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N2_mature_unmapped.fq.gz").exists(), path("$outputDir/mirna_quant/bam/mature/unmapped/Clone1_N1_mature_unmapped.fq.gz").exists(), path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N1_mature_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone9_N2_mature_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/mature/unmapped/Clone1_N3_mature_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N2_mature_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.tsv").exists(), + path("$outputDir/mirna_quant/bam/mature/unmapped/Control_N3_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N2_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N2_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N3_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N3_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N1_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N2_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone1_N1_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Clone9_N1_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/Control_N3_mature_hairpin_unmapped.fq.gz").exists() + ).match("mirna_quant_bam") }, + + { assert snapshot( path("$outputDir/mirna_quant/mirtop/mirtop.gff").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop.tsv").exists(), path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists(), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Control_N2.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists() + ).match("mirna_quant_mirtop") }, + + { assert snapshot( + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists() - ).match("mirna_quant") }, + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists() + ).match("mirna_quant_edger_qc") }, { assert snapshot( - path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Clone9_N3.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Clone9_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Control_N1.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Control_N3.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/Control_N2.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip").exists(), path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone9_N2.raw_fastqc.zip").exists() + ).match("fastqc_raw") }, + + { assert snapshot( + path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip").exists(), path("$outputDir/fastqc/trimmed/Clone9_N3.trim_fastqc.zip").exists(), path("$outputDir/fastqc/trimmed/Clone9_N2.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip").exists(), path("$outputDir/fastqc/trimmed/Clone1_N1.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Control_N2.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Control_N1.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/Clone1_N3.trim_fastqc.zip").exists() - ).match("fastqc") }, + path("$outputDir/fastqc/trimmed/Clone9_N1.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/Control_N3.trim_fastqc.zip").exists() + ).match("fastqc_trimmed") }, { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-phred.tsv") + ).match("mirtrace") }, + + { assert snapshot( path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N3.fastp.fasta"), @@ -278,7 +237,10 @@ nextflow_pipeline { path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N2.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N2.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N3.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta") + ).match("mirtrace_qc_passed_reads.all.collapsed") }, + + { assert snapshot( path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N3.fastp.fasta"), @@ -287,7 +249,70 @@ nextflow_pipeline { path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N2.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N3.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") - ).match("mirtrace") }, + ).match("mirtrace_qc_passed_reads.rnatype_unknown.collapsed") }, + + { assert snapshot( + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt") + ).match("bowtie_index_mirna_mature") }, + + { assert snapshot( + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt") + ).match("bowtie_index_mirna_hairpin") }, + + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), + path("$outputDir/multiqc/multiqc_data/fastp_filtered_reads_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-quality-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_adapter_content_plot-1.txt"), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_Before_filtering.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") + ).match("multiqc_multiqc_data") }, ) } diff --git a/tests/test_technical_repeats.nf.test b/tests/test_technical_repeats.nf.test index 1325e605..9ee71761 100644 --- a/tests/test_technical_repeats.nf.test +++ b/tests/test_technical_repeats.nf.test @@ -1,3 +1,4 @@ + nextflow_pipeline { name "Test Workflow main.nf - test_technical_repeats" @@ -24,118 +25,142 @@ nextflow_pipeline { path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), path("$outputDir/bowtie_index/genome/genome.2.ebwt"), path("$outputDir/bowtie_index/genome/genome.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.edited.fa"), path("$outputDir/bowtie_index/genome/genome.3.ebwt"), path("$outputDir/bowtie_index/genome/genome.4.ebwt"), path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/genome/genome.edited.fa") + ).match("bowtie_index_genome") }, + + { assert snapshot( path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt") + ).match("bowtie_index_mirna_mature") }, { assert snapshot( - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai").exists() - ).match("genome_quant") }, + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt") + ).match("bowtie_index_mirna_hairpin") }, + + { assert snapshot( + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa") + ).match("mirna_quant_reference") }, + + { assert snapshot( + path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz") + ).match("mirna_quant_seqcluster") }, { assert snapshot( - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.tsv").exists(), + path("$outputDir/mirna_quant/bam/mature/Control_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone9_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone9_N3_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Control_N1_mature_hairpin.sorted.stats") + ).match("mirna_quant_bam") }, + + { assert snapshot( path("$outputDir/mirna_quant/mirtop/mirtop.gff").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop.tsv").exists(), path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists(), - path("$outputDir/mirna_quant/seqcluster/final/Control_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone1_N1.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/Clone9_N3.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists() + ).match("mirna_quant_mirtop") }, + + { assert snapshot( + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_plot_coordinates.txt").exists(), path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_log2CPM_sample_distances.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_distance_matrix.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_edgeR_MDS_plot_coordinates.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists() - ).match("mirna_quant") }, + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists() + ).match("mirna_quant_edger_qc") }, { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta"), + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv") + ).match("mirtrace") }, + + { assert snapshot( path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone1_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Control_N1.fastp.fasta"), path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/Clone9_N3.fastp.fasta") - ).match("mirtrace") }, + ).match("mirtrace_qc_passed_reads.rnatype_unknown.collapsed") }, + + { assert snapshot( + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone1_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Control_N1.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/Clone9_N3.fastp.fasta") + ).match("mirtrace_qc_passed_reads.all.collapsed") }, + + { assert snapshot( + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/Clone9_N3_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Control_N1_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/Clone1_N1_mature_hairpin_genome.sorted.stats") + ).match("genome_quant_bam") }, ) } diff --git a/tests/test_umi.nf.test b/tests/test_umi.nf.test index e3ba0b12..e8d3bdfa 100644 --- a/tests/test_umi.nf.test +++ b/tests/test_umi.nf.test @@ -1,3 +1,4 @@ + nextflow_pipeline { name "Test Workflow main.nf - test_umi" @@ -21,26 +22,153 @@ nextflow_pipeline { { assert workflow.trace.succeeded().size() == 64 }, { assert snapshot( - path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), - path("$outputDir/bowtie_index/genome/genome.2.ebwt"), path("$outputDir/bowtie_index/genome/genome.1.ebwt"), - path("$outputDir/bowtie_index/genome/genome.edited.fa"), - path("$outputDir/bowtie_index/genome/genome.3.ebwt"), path("$outputDir/bowtie_index/genome/genome.4.ebwt"), + path("$outputDir/bowtie_index/genome/genome.edited.fa"), + path("$outputDir/bowtie_index/genome/genome.rev.2.ebwt"), path("$outputDir/bowtie_index/genome/genome.rev.1.ebwt"), + path("$outputDir/bowtie_index/genome/genome.2.ebwt"), + path("$outputDir/bowtie_index/genome/genome.3.ebwt") + ).match("bowtie_index_genome") }, + + { assert snapshot( + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt") + ).match("bowtie_index_mirna_hairpin") }, + + { assert snapshot( path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), - path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt") - ).match("bowtie_index") }, + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt") + ).match("bowtie_index_mirna_mature") }, + + { assert snapshot( + path("$outputDir/fastqc/raw/SRX8195118_SRR11631014.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/SRX8195117_SRR11631013.raw_fastqc.zip").exists() + ).match("fastqc_raw") }, + + { assert snapshot( + path("$outputDir/fastqc/trimmed/SRX8195118_SRR11631014.trim_fastqc.zip").exists(), + path("$outputDir/fastqc/trimmed/SRX8195117_SRR11631013.trim_fastqc.zip").exists() + ).match("fastqc_trimmed") }, + + { assert snapshot( + path("$outputDir/umi_dedup/bam_deduplicated/SRX8195118_SRR11631014.umi_dedup.sorted.fastq.gz"), + path("$outputDir/umi_dedup/bam_deduplicated/SRX8195117_SRR11631013.umi_dedup.sorted.fastq.gz") + ).match("umi_dedup_bam_deduplicated") }, + + { assert snapshot( + path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195118_SRR11631014.umi_extract.fastq.gz"), + path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195117_SRR11631013.umi_extract.fastq.gz") + ).match("umi_dedup_fastq_extracted_umi") }, + + { assert snapshot( + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa") + ).match("mirna_quant_reference") }, + + { assert snapshot( + path("$outputDir/mirna_quant/seqcluster/final/SRX8195118_SRR11631014.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/SRX8195117_SRR11631013.fastp_trimmed.fastq.gz") + ).match("mirna_quant_seqcluster") }, + + { assert snapshot( + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195118_SRR11631014_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195117_SRR11631013_mature_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/SRX8195118_SRR11631014_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/SRX8195117_SRR11631013_seqcluster.bam").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195118_SRR11631014_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195117_SRR11631013_seqcluster_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/SRX8195118_SRR11631014_mature_hairpin_unmapped.fq.gz").exists(), + path("$outputDir/mirna_quant/bam/hairpin/unmapped/SRX8195117_SRR11631013_mature_hairpin_unmapped.fq.gz").exists() + ).match("mirna_quant_bam") }, + + { assert snapshot( + path("$outputDir/mirna_quant/mirtop/mirtop.gff").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop.tsv").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists() + ).match("mirna_quant_mirtop") }, + + { assert snapshot( + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists() + ).match("mirna_quant_edger_qc") }, + + { assert snapshot( + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv") + ).match("mirtrace") }, + + { assert snapshot( + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/SRX8195118_SRR11631014.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/SRX8195117_SRR11631013.fastp.fasta") + ).match("mirtrace_qc_passed_reads.all.collapsed") }, + + { assert snapshot( + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/SRX8195118_SRR11631014.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/SRX8195117_SRR11631013.fastp.fasta") + ).match("mirtrace_qc_passed_reads.rnatype_unknown.collapsed") }, + + { assert snapshot( + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam").exists(), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam.bai").exists(), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat"), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats"), + path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats"), + path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats") + ).match("genome_quant_bam") }, { assert snapshot( path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), @@ -84,104 +212,7 @@ nextflow_pipeline { path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists(), path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") - ).match("multiqc") }, - - { assert snapshot( - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.flagstat"), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.bam.bai").exists(), - path("$outputDir/genome_quant/bam/SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats"), - path("$outputDir/genome_quant/bam/SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats") - ).match("genome_quant") }, - - { assert snapshot( - path("$outputDir/umi_dedup/bam_deduplicated/SRX8195117_SRR11631013.umi_dedup.sorted.fastq.gz"), - path("$outputDir/umi_dedup/bam_deduplicated/SRX8195118_SRR11631014.umi_dedup.sorted.fastq.gz"), - path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195118_SRR11631014.umi_extract.fastq.gz"), - path("$outputDir/umi_dedup/fastq_extracted_umi/SRX8195117_SRR11631013.umi_extract.fastq.gz") - ).match("umi_dedup") }, - - { assert snapshot( - path("$outputDir/mirna_quant/bam/seqcluster/SRX8195117_SRR11631013_seqcluster.bam").exists(), - path("$outputDir/mirna_quant/bam/seqcluster/SRX8195118_SRR11631014_seqcluster.bam").exists(), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195117_SRR11631013_seqcluster_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/seqcluster/unmapped/SRX8195118_SRR11631014_seqcluster_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195118_SRR11631014_mature_hairpin.sorted.stats"), - path("$outputDir/mirna_quant/bam/hairpin/SRX8195117_SRR11631013_mature_hairpin.bam").exists(), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/SRX8195118_SRR11631014_mature_hairpin_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/hairpin/unmapped/SRX8195117_SRR11631013_mature_hairpin_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.flagstat"), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.stats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.sorted.idxstats"), - path("$outputDir/mirna_quant/bam/mature/SRX8195118_SRR11631014_mature.sorted.bam.bai").exists(), - path("$outputDir/mirna_quant/bam/mature/SRX8195117_SRR11631013_mature.bam").exists(), - path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195118_SRR11631014_mature_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/bam/mature/unmapped/SRX8195117_SRR11631013_mature_unmapped.fq.gz").exists(), - path("$outputDir/mirna_quant/mirtop/mirna.tsv"), - path("$outputDir/mirna_quant/mirtop/mirtop.tsv").exists(), - path("$outputDir/mirna_quant/mirtop/mirtop.gff").exists(), - path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), - path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists(), - path("$outputDir/mirna_quant/seqcluster/final/SRX8195117_SRR11631013.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/seqcluster/final/SRX8195118_SRR11631014.fastp_trimmed.fastq.gz"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa"), - path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), - path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), - path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), - path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), - path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists() - ).match("mirna_quant") }, - - { assert snapshot( - path("$outputDir/fastqc/raw/SRX8195117_SRR11631013.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/raw/SRX8195118_SRR11631014.raw_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/SRX8195117_SRR11631013.trim_fastqc.zip").exists(), - path("$outputDir/fastqc/trimmed/SRX8195118_SRR11631014.trim_fastqc.zip").exists() - ).match("fastqc") }, - - { assert snapshot( - path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), - path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/SRX8195118_SRR11631014.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/SRX8195117_SRR11631013.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/SRX8195118_SRR11631014.fastp.fasta"), - path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/SRX8195117_SRR11631013.fastp.fasta") - ).match("mirtrace") }, + ).match("multiqc_multiqc_data") }, ) } From e307076e86ea454fcd1ed3e453aa32c78ebd7125 Mon Sep 17 00:00:00 2001 From: zxBIB Schcolnicov Date: Thu, 22 Aug 2024 22:58:57 +0200 Subject: [PATCH 09/15] Updated snaps --- tests/test.nf.test.snap | 431 +++++++++++++--------- tests/test_index.nf.test.snap | 33 +- tests/test_mirgenedb.nf.test.snap | 346 +++++++++-------- tests/test_no_genome.nf.test.snap | 396 ++++++++++++-------- tests/test_technical_repeats.nf.test.snap | 216 +++++++---- tests/test_umi.nf.test.snap | 280 +++++++++----- 6 files changed, 1035 insertions(+), 667 deletions(-) diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap index 3f49d724..43c24334 100644 --- a/tests/test.nf.test.snap +++ b/tests/test.nf.test.snap @@ -1,124 +1,166 @@ { - "bowtie_index": { + "fastqc_trimmed": { + "content": [ + true, + true, + true, + true, + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T22:51:48.886414317" + }, + "bowtie_index_genome": { "content": [ - "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", "genome.2.ebwt:md5,8f007efb2d23e46035cc47340c4d981e", - "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", - "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", "genome.3.ebwt:md5,caf97e67055e1b465e933214d0168e68", + "genome.1.ebwt:md5,1bfbf95848b5a2e8a786d0a2c1054bbb", + "genome.rev.2.ebwt:md5,65f054c598e3e9fdd33cb22c9f8f8ca5", "genome.4.ebwt:md5,87ff9d3ef8b55f845a9205a19c729f1c", - "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", - "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", - "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", - "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", - "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", - "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", - "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", - "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", - "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", - "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", - "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", - "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", - "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f" + "genome.edited.fa:md5,5aaada29b1c575230fa1b7c3bd4d76db", + "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff" ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-20T19:07:54.749575939" + "timestamp": "2024-08-22T22:51:16.37660337" }, "mirtrace": { "content": [ - "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", + "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", - "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", - "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", + "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", - "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638", - "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", - "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", - "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", - "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", - "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", - "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", - "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", - "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8", - 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"nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T22:52:09.114139077" + }, + "genome_quant_bam": { + "content": [ + true, + true, + true, true, true, true, @@ -306,14 +305,96 @@ true, true, true, + "Clone9_N2_mature_hairpin_genome.sorted.flagstat:md5,b8fbbdaca0458b19732312dea2997be8", + "Control_N3_mature_hairpin_genome.sorted.stats:md5,53e8fca566dd5dd8553b25c38e961f6b", + "Clone1_N1_mature_hairpin_genome.sorted.flagstat:md5,4d552770e6d3b06775b6f484684f7a77", + "Clone9_N1_mature_hairpin_genome.sorted.stats:md5,f819db926f570a9bb1cf9b6adff7d758", + "Clone9_N1_mature_hairpin_genome.sorted.flagstat:md5,2fd8cd41edde2292f857528658c3e0a1", + "Clone1_N1_mature_hairpin_genome.sorted.stats:md5,64b19984a4c2fa55e69a28fe7c138d7c", + "Clone1_N3_mature_hairpin_genome.sorted.flagstat:md5,9dee041c82ad3b2d2ab4f8986822f2ce", + "Control_N1_mature_hairpin_genome.sorted.flagstat:md5,18f0028f1cfc137ef8f089e465fe20f5", + "Control_N3_mature_hairpin_genome.sorted.flagstat:md5,ae834e3dbaa18aa9bce66c3b0034c430", + "Clone9_N1_mature_hairpin_genome.sorted.idxstats:md5,a199f8999ba915a81acfc450e0db8393", + "Clone9_N2_mature_hairpin_genome.sorted.stats:md5,6db5d451fa95a77247d38c4a263cf05d", + "Clone9_N3_mature_hairpin_genome.sorted.idxstats:md5,0a227abfa6aa10023219bce7b2795b67", + "Control_N2_mature_hairpin_genome.sorted.stats:md5,f105861208044e44644c74449d0c6142", + "Control_N1_mature_hairpin_genome.sorted.idxstats:md5,fe01b41ed88612c28b667817c4a8fcc1", + "Control_N2_mature_hairpin_genome.sorted.idxstats:md5,b6da32ce230fdeab39f3c4d5dcf41a3a", + "Control_N1_mature_hairpin_genome.sorted.stats:md5,b2afcfcb9e785a71bb5fce25b87fd67a", + "Control_N2_mature_hairpin_genome.sorted.flagstat:md5,b0d42e94b2e0e026cd32a88dce40722c", + "Clone9_N3_mature_hairpin_genome.sorted.stats:md5,8ec73033ee0e2ad16fdc497b209adb50", + "Clone9_N2_mature_hairpin_genome.sorted.idxstats:md5,61c4821cba66c91272e62547617db2c9", + "Clone1_N1_mature_hairpin_genome.sorted.idxstats:md5,169a196ee2da6945392f6a361164ffc5", + "Clone1_N3_mature_hairpin_genome.sorted.stats:md5,fb089da3351a3f8c0bc742f3f4533349", + "Control_N3_mature_hairpin_genome.sorted.idxstats:md5,94d53c9ad335779a1ea25fd5b4b08069", + "Clone1_N3_mature_hairpin_genome.sorted.idxstats:md5,d680e48370d319f1891cdd61b8754644", + "Clone9_N3_mature_hairpin_genome.sorted.flagstat:md5,dbe38679a68d55b8a182831e336eebb1" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T22:52:20.338493953" + }, + "bowtie_index_mirna_mature": { + "content": [ + "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", + "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f", + "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", + "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", + "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", + "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T22:51:16.994060474" + }, + "bowtie_index_mirna_hairpin": { + "content": [ + "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", + "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", + "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", + "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", + "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", + "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T22:51:17.519448134" + }, + "mirtrace_qc_passed_reads.all.collapsed": { + "content": [ + "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", + "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", + "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", + "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", + "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", + "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", + "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", + "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T22:51:59.69892856" + }, + "mirna_quant_mirtop": { + "content": [ + "mirtop_rawData.tsv:md5,774410dd2cf1e5be83bf8d6e1e8b96b0", true, true, + "mirna.tsv:md5,1f840afe7ab68eac73feaaad321b64f6", true ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T13:46:30.62317228" + "timestamp": "2024-08-22T22:51:32.899870265" } } \ No newline at end of file diff --git a/tests/test_index.nf.test.snap b/tests/test_index.nf.test.snap index 3cb0d6ba..9e0ecf46 100644 --- a/tests/test_index.nf.test.snap +++ b/tests/test_index.nf.test.snap @@ -14,7 +14,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:07:36.900487683" + "timestamp": "2024-08-22T22:10:36.718345249" }, "mirtrace": { "content": [ @@ -30,7 +30,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:07:50.05985187" + "timestamp": "2024-08-22T22:10:40.727064117" }, "mirna_quant_reference": { "content": [ @@ -43,7 +43,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:06:50.940201041" + "timestamp": "2024-08-22T22:10:00.32667588" }, "software_versions": { "content": [ @@ -53,7 +53,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:06:50.443184087" + "timestamp": "2024-08-22T22:09:59.767390635" }, "mirna_quant_bam": { "content": [ @@ -142,7 +142,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:06:56.681862113" + "timestamp": "2024-08-22T22:10:09.479500085" }, "mirna_quant_edger_qc": { "content": [ @@ -167,7 +167,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:07:13.417967341" + "timestamp": "2024-08-22T22:10:23.564610058" }, "fastqc_raw": { "content": [ @@ -184,7 +184,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:07:23.201927758" + "timestamp": "2024-08-22T22:10:28.885128861" }, "multiqc_multiqc_data": { "content": [ @@ -235,7 +235,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:10:00.492463242" + "timestamp": "2024-08-22T22:11:37.214190607" }, "untar_bowtie_index": { "content": [ @@ -250,7 +250,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:06:50.464299168" + "timestamp": "2024-08-22T22:09:59.790457982" }, "mirna_quant_seqcluster": { "content": [ @@ -267,7 +267,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:06:51.076830741" + "timestamp": "2024-08-22T22:10:00.453230388" }, "mirtrace_qc_passed_reads.rnatype_unknown.collapsed": { "content": [ @@ -284,13 +284,12 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:08:39.709442943" + "timestamp": "2024-08-22T22:10:57.082105969" }, "genome_quant_bam": { "content": [ true, true, - "Control_N2_mature_hairpin_genome.sorted.flagstat:md5,b0d42e94b2e0e026cd32a88dce40722c", "Control_N2_mature_hairpin_genome.sorted.idxstats:md5,b6da32ce230fdeab39f3c4d5dcf41a3a", "Control_N2_mature_hairpin_genome.sorted.stats:md5,1222b755feaf406ecea3f2abb35a737c" ], @@ -298,7 +297,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:09:49.007300611" + "timestamp": "2024-08-22T22:11:26.415029668" }, "bowtie_index_mirna_mature": { "content": [ @@ -313,7 +312,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:09:14.547618596" + "timestamp": "2024-08-22T22:11:09.207867519" }, "bowtie_index_mirna_hairpin": { "content": [ @@ -328,7 +327,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:09:27.72464599" + "timestamp": "2024-08-22T22:11:17.523064067" }, "mirtrace_qc_passed_reads.all.collapsed": { "content": [ @@ -345,7 +344,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:07:59.93600436" + "timestamp": "2024-08-22T22:10:45.973826356" }, "mirna_quant_mirtop": { "content": [ @@ -359,6 +358,6 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T19:07:04.940104262" + "timestamp": "2024-08-22T22:10:16.715546319" } } \ No newline at end of file diff --git a/tests/test_mirgenedb.nf.test.snap b/tests/test_mirgenedb.nf.test.snap index 8aee6b90..96818b72 100644 --- a/tests/test_mirgenedb.nf.test.snap +++ b/tests/test_mirgenedb.nf.test.snap @@ -1,33 +1,38 @@ { - "bowtie_index": { + "fastqc_trimmed": { "content": [ + true, + true, + true, + true, + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T22:43:10.283525327" + }, + "bowtie_index_genome": { + "content": [ + "genome.rev.1.ebwt:md5,3275dafaca50d8cafde473b54e9ebbff", 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"2024-08-22T22:52:32.630636315" + }, + "genome_quant_bam": { + "content": [ true, true, true, true, + "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.flagstat:md5,235383f64a943885f5d899f5b8e03eba", + "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.flagstat:md5,977e88cbe62027285df73e1f7f9cd9bc", + "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.idxstats:md5,a4874de294706a7ead30258944ff2dad", + "SRX8195118_SRR11631014_mature_hairpin_genome.sorted.stats:md5,e19093f62044a7d053a0073092c506f3", + "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.stats:md5,053912820064080299710bfbe7baf3c7", + "SRX8195117_SRR11631013_mature_hairpin_genome.sorted.idxstats:md5,cc0413bf90252c3b3af8926fd64bc873" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T22:52:39.634115257" + }, + "umi_dedup_bam_deduplicated": { + "content": [ + "SRX8195118_SRR11631014.umi_dedup.sorted.fastq.gz:md5,af2b98d9bd6d0760a7eb07813d015aee", + "SRX8195117_SRR11631013.umi_dedup.sorted.fastq.gz:md5,247d78a2d700012064d0b2e28d04b061" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T22:51:20.189322584" + }, + "bowtie_index_mirna_mature": { + "content": [ + "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", + "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", + "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f", + "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", + "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18", + "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T22:51:17.603519295" + }, + "bowtie_index_mirna_hairpin": { + "content": [ + "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", + "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", + "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", + "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", + "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62", + "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T22:51:17.150913158" + }, + "mirtrace_qc_passed_reads.all.collapsed": { + "content": [ + "SRX8195118_SRR11631014.fastp.fasta:md5,99e2ce92ce102bd3fedc3a9d3b926873", + "SRX8195117_SRR11631013.fastp.fasta:md5,e0e31d882568a7853dea75b3c595108f" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-22T22:52:22.862929991" + }, + "mirna_quant_mirtop": { + "content": [ true, true, + "mirtop_rawData.tsv:md5,ed4a0ceb2e8cd1721aa5ed27270f9623", + "mirna.tsv:md5,e30f3037522a0a20f2a4b32cbb70990a", true ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-21T21:46:44.500946722" + "timestamp": "2024-08-22T22:51:59.309623574" } } \ No newline at end of file From 5638e24d0cfaf4cd96474a1b3c8f587c5256b215 Mon Sep 17 00:00:00 2001 From: zxBIB Schcolnicov Date: Fri, 23 Aug 2024 15:08:12 +0200 Subject: [PATCH 10/15] Updated test_index to work in CI --- tests/test_index.nf.test | 14 +++++++------- tests/test_index.nf.test.snap | 13 ------------- 2 files changed, 7 insertions(+), 20 deletions(-) diff --git a/tests/test_index.nf.test b/tests/test_index.nf.test index 481d56e1..2a2b11fd 100644 --- a/tests/test_index.nf.test +++ b/tests/test_index.nf.test @@ -229,13 +229,13 @@ nextflow_pipeline { path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt") ).match("bowtie_index_mirna_hairpin") }, - { assert snapshot( - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists(), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), - //path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), //this file is outputed by the profile but it is not outputed while running CI tests - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), - path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats") - ).match("genome_quant_bam") }, + // { assert snapshot( //these files are outputed by the profile but are sometimes not outputed while running CI tests + // path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists(), + // path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), + // path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), + // path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), + // path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats") + // ).match("genome_quant_bam") }, { assert snapshot( path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), diff --git a/tests/test_index.nf.test.snap b/tests/test_index.nf.test.snap index 9e0ecf46..2d35b6f4 100644 --- a/tests/test_index.nf.test.snap +++ b/tests/test_index.nf.test.snap @@ -286,19 +286,6 @@ }, "timestamp": "2024-08-22T22:10:57.082105969" }, - "genome_quant_bam": { - "content": [ - true, - true, - "Control_N2_mature_hairpin_genome.sorted.idxstats:md5,b6da32ce230fdeab39f3c4d5dcf41a3a", - "Control_N2_mature_hairpin_genome.sorted.stats:md5,1222b755feaf406ecea3f2abb35a737c" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" - }, - "timestamp": "2024-08-22T22:11:26.415029668" - }, "bowtie_index_mirna_mature": { "content": [ "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", From 003eb34bff3f47e47f08507ac0ea4592be515650 Mon Sep 17 00:00:00 2001 From: zxBIB Schcolnicov Date: Fri, 23 Aug 2024 17:51:24 +0200 Subject: [PATCH 11/15] Adapted params to work with ingested datasets --- nextflow.config | 4 ++-- nextflow_schema.json | 4 ++-- workflows/smrnaseq.nf | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/nextflow.config b/nextflow.config index 8597ece8..d5f34d40 100644 --- a/nextflow.config +++ b/nextflow.config @@ -21,8 +21,8 @@ params { igenomes_base = 's3://ngi-igenomes/igenomes' igenomes_ignore = false mirna_gtf = null - mature = "https://mirbase.org/download/mature.fa" - hairpin = "https://mirbase.org/download/hairpin.fa" + mature = "https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/mature.fa" + hairpin = "https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/hairpin.fa" mirgenedb = false mirgenedb_mature = null mirgenedb_hairpin = null diff --git a/nextflow_schema.json b/nextflow_schema.json index db28ef7f..6c394193 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -154,7 +154,7 @@ "description": "Path to FASTA file with mature miRNAs.", "fa_icon": "fas fa-wheelchair", "help_text": "Typically this will be the `mature.fa` file from miRBase. Can be given either as a plain text `.fa` file or a compressed `.gz` file.\n\nDefaults to the current miRBase release URL, from which the file will be downloaded.", - "default": "https://mirbase.org/download/mature.fa" + "default": "https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/mature.fa" }, "mirgenedb_mature": { "type": "string", @@ -166,7 +166,7 @@ "description": "Path to FASTA file with miRNAs precursors.", "fa_icon": "fab fa-cuttlefish", "help_text": "Typically this will be the `mature.fa` file from miRBase. Can be given either as a plain text `.fa` file or a compressed `.gz` file.\n\nDefaults to the current miRBase release URL, from which the file will be downloaded.", - "default": "https://mirbase.org/download/hairpin.fa" + "default": "https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/hairpin.fa" }, "mirgenedb_hairpin": { "type": "string", diff --git a/workflows/smrnaseq.nf b/workflows/smrnaseq.nf index ac410b8f..c6c9af0b 100644 --- a/workflows/smrnaseq.nf +++ b/workflows/smrnaseq.nf @@ -53,7 +53,7 @@ workflow NFCORE_SMRNASEQ { } // Genome options - def mirna_gtf_from_species = params.mirtrace_species ? "https://mirbase.org/download/CURRENT/genomes/${params.mirtrace_species}.gff3" : false + def mirna_gtf_from_species = params.mirtrace_species ? (params.mirtrace_species == 'hsa' ? "https://github.com/nf-core/test-datasets/raw/smrnaseq/miRBase/hsa.gff3" : "https://mirbase.org/download/CURRENT/genomes/${params.mirtrace_species}.gff3") : false def mirna_gtf = params.mirna_gtf ?: mirna_gtf_from_species if (!params.mirgenedb) { From 91d18a0172ccc82702d4f66b1924912e670ffef8 Mon Sep 17 00:00:00 2001 From: zxBIB Schcolnicov Date: Fri, 23 Aug 2024 18:17:51 +0200 Subject: [PATCH 12/15] Fixed pre-commit --- tests/test_index.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_index.nf.test b/tests/test_index.nf.test index 2a2b11fd..9800888a 100644 --- a/tests/test_index.nf.test +++ b/tests/test_index.nf.test @@ -232,7 +232,7 @@ nextflow_pipeline { // { assert snapshot( //these files are outputed by the profile but are sometimes not outputed while running CI tests // path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam").exists(), // path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.bam.bai").exists(), - // path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), + // path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.flagstat"), // path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.idxstats"), // path("$outputDir/genome_quant/bam/Control_N2_mature_hairpin_genome.sorted.stats") // ).match("genome_quant_bam") }, From 46ed8de9599c52cb8c61372a16535eef2d03777f Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Sat, 24 Aug 2024 18:30:38 +0000 Subject: [PATCH 13/15] Using nf-test version 0.9.0 in ci --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 41843f15..df639239 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -11,7 +11,7 @@ on: env: NXF_ANSI_LOG: false CAPSULE_LOG: none - NFTEST_VER: "0.8.4" + NFTEST_VER: "0.9.0" concurrency: group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" From 92c289d0fcc29fe22814936bba936129bba6bfaf Mon Sep 17 00:00:00 2001 From: zxBIB Schcolnicov Date: Mon, 26 Aug 2024 14:12:18 +0200 Subject: [PATCH 14/15] Added skipfastp nftest --- tests/test_skipfastp.nf.test | 154 ++++++++++++++++++++++ tests/test_skipfastp.nf.test.snap | 209 ++++++++++++++++++++++++++++++ 2 files changed, 363 insertions(+) create mode 100644 tests/test_skipfastp.nf.test create mode 100644 tests/test_skipfastp.nf.test.snap diff --git a/tests/test_skipfastp.nf.test b/tests/test_skipfastp.nf.test new file mode 100644 index 00000000..7eae6e2c --- /dev/null +++ b/tests/test_skipfastp.nf.test @@ -0,0 +1,154 @@ + +nextflow_pipeline { + + name "Test Workflow main.nf - test_skipfastp" + script "main.nf" + profile "test_skipfastp" + tag "test_skipfastp" + tag "pipeline" + + test("test_skipfastp") { + + when { + params { + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, + { assert workflow.trace.succeeded().size() == 41 }, + + { assert snapshot( + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa"), + path("$outputDir/mirna_quant/reference/hairpin.fa_igenome.fa_idx.fa"), + path("$outputDir/mirna_quant/reference/mature.fa_igenome.fa_idx.fa") + ).match("mirna_quant_reference") }, + + { assert snapshot( + path("$outputDir/mirna_quant/seqcluster/final/small_Clone1_N3.fastp_trimmed.fastq.gz"), + path("$outputDir/mirna_quant/seqcluster/final/small_Clone1_N1.fastp_trimmed.fastq.gz") + ).match("mirna_quant_seqcluster") }, + + { assert snapshot( + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.stats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N3_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/mature/Clone1_N1_mature.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.bam.bai").exists(), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.stats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N1_mature_hairpin.sorted.idxstats"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.flagstat"), + path("$outputDir/mirna_quant/bam/hairpin/Clone1_N3_mature_hairpin.sorted.idxstats") + ).match("mirna_quant_bam") }, + + { assert snapshot( + path("$outputDir/mirna_quant/mirtop/mirtop.tsv").exists(), + path("$outputDir/mirna_quant/mirtop/mirtop_rawData.tsv"), + path("$outputDir/mirna_quant/mirtop/mirtop.gff").exists(), + path("$outputDir/mirna_quant/mirtop/mirna.tsv"), + path("$outputDir/mirna_quant/mirtop/stats/mirtop_stats.txt").exists() + ).match("mirna_quant_mirtop") }, + + { assert snapshot( + path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/hairpin_normalized_CPM.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_logtpm.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_unmapped_read_counts.txt").exists(), + path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists() + ).match("mirna_quant_edger_qc") }, + + { assert snapshot( + path("$outputDir/fastqc/raw/Clone1_N1.raw_fastqc.zip").exists(), + path("$outputDir/fastqc/raw/Clone1_N3.raw_fastqc.zip").exists() + ).match("fastqc_raw") }, + + { assert snapshot( + path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-rnatype.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-phred.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-contamination_detailed.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-length.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-qcstatus.tsv"), + path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv") + ).match("mirtrace") }, + + { assert snapshot( + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/small_Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.all.collapsed/small_Clone1_N1.fastp.fasta") + ).match("mirtrace_qc_passed_reads.all.collapsed") }, + + { assert snapshot( + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/small_Clone1_N3.fastp.fasta"), + path("$outputDir/mirtrace/qc_passed_reads.rnatype_unknown.collapsed/small_Clone1_N1.fastp.fasta") + ).match("mirtrace_qc_passed_reads.rnatype_unknown.collapsed") }, + + { assert snapshot( + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_hairpin/fasta_bidx.rev.1.ebwt") + ).match("bowtie_index_mirna_hairpin") }, + + { assert snapshot( + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.1.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.4.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.3.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.2.ebwt"), + path("$outputDir/bowtie_index/mirna_mature/fasta_bidx.rev.1.ebwt") + ).match("bowtie_index_mirna_mature") }, + + { assert snapshot( + path("$outputDir/multiqc/multiqc_data/fastqc-status-check-heatmap.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_complexity_plot.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_citations.txt"), + path("$outputDir/multiqc/multiqc_data/samtools-stats-dp.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_general_stats.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_qc_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_length_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtrace_rna_categories_plot.txt"), + path("$outputDir/multiqc/multiqc_data/samtools_alignment_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("$outputDir/multiqc/multiqc_data/mirtop_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/mirtop_unique_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/mirtop_mean_read_count_plot.txt").exists(), + path("$outputDir/multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("$outputDir/multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("$outputDir/multiqc/multiqc_data/multiqc_sources.txt").exists() + ).match("multiqc_multiqc_data") }, + + ) + } + + } + +} diff --git a/tests/test_skipfastp.nf.test.snap b/tests/test_skipfastp.nf.test.snap new file mode 100644 index 00000000..0b5df662 --- /dev/null +++ b/tests/test_skipfastp.nf.test.snap @@ -0,0 +1,209 @@ +{ + "mirtrace": { + "content": [ + "mirtrace-stats-contamination_basic.tsv:md5,af4ef7d436a78b63ebbdbd5736757736", + "mirtrace-stats-rnatype.tsv:md5,c7cb1b388ecd16ae79e1ebdf8d896342", + "mirtrace-stats-phred.tsv:md5,a56d0e1fd11b9284b9705bed63b30c02", + "mirtrace-stats-contamination_detailed.tsv:md5,4aa73df82130f7cf2d056b4c61cd9d2a", + "mirtrace-stats-length.tsv:md5,48e4ec1a5572c2f4f58355125b95f614", + "mirtrace-stats-qcstatus.tsv:md5,9f8357437ea532505d3f3a461be476b0", + "mirtrace-stats-mirna-complexity.tsv:md5,761ad553ef141cb5f7845cf476b323d9" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-26T13:38:39.961892895" + }, + "mirna_quant_reference": { + "content": [ + "hairpin.fa_igenome.fa:md5,5fb538f60d5288846600dba31010251e", + "mature.fa_igenome.fa:md5,ef4cabcbea05adf334ba6891a50c951a", + "hairpin.fa_igenome.fa_idx.fa:md5,482b0327b0c1e36748c1ee3d3be9be77", + "mature.fa_igenome.fa_idx.fa:md5,ef4cabcbea05adf334ba6891a50c951a" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-26T13:38:35.976877813" + }, + "software_versions": { + "content": [ + "{BOWTIE_MAP_HAIRPIN={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_MATURE={bowtie=1.3.1, samtools=1.14}, BOWTIE_MAP_SEQCLUSTER={bowtie=1.3.1, samtools=1.14}, FASTQC_RAW={fastqc=0.12.1}, FORMAT_HAIRPIN={fastx_toolkit=0.0.14}, FORMAT_MATURE={fastx_toolkit=0.0.14}, INDEX_HAIRPIN={bowtie=1.3.1}, INDEX_MATURE={bowtie=1.3.1}, MIRTOP_QUANT={mirtop=0.4.25}, MIRTRACE_RUN={mirtrace=1.0.1}, PARSE_HAIRPIN={seqkit=2.6.1}, PARSE_MATURE={seqkit=2.6.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SEQCLUSTER_SEQUENCES={seqcluster=1.2.9}, TABLE_MERGE={r-base=3.6.2}, Workflow={nf-core/smrnaseq=v2.3.2dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-26T13:38:35.931631908" + }, + "mirna_quant_bam": { + "content": [ + true, + true, + true, + true, + "Clone1_N3_mature.sorted.stats:md5,e028b49e804c55056fca34090cd3d836", + "Clone1_N1_mature.sorted.stats:md5,ae056e94e36c06b35913ae8f9268a473", + "Clone1_N1_mature.sorted.idxstats:md5,4c3722c4eee312a587e3aea26d240696", + "Clone1_N3_mature.sorted.idxstats:md5,bde0293f0938a8a074ad3ac633d8cb73", + "Clone1_N3_mature.sorted.flagstat:md5,9e287eb7ac83624b262864d0255217fd", + "Clone1_N1_mature.sorted.flagstat:md5,f8dd1a5032573e17558964260346c6be", + true, + true, + true, + true, + "Clone1_N1_mature_hairpin.sorted.flagstat:md5,883a0e9f52c4c876ef9847daa63ec0de", + "Clone1_N3_mature_hairpin.sorted.stats:md5,4fbda712e789f98124583069f4f35187", + "Clone1_N1_mature_hairpin.sorted.stats:md5,6f355f21f06071dd5751491a9eb355ef", + "Clone1_N1_mature_hairpin.sorted.idxstats:md5,6601b61f1c8a343ba901f328eb2499ed", + "Clone1_N3_mature_hairpin.sorted.flagstat:md5,1630edf055b591303d7c68d013745938", + "Clone1_N3_mature_hairpin.sorted.idxstats:md5,b44fb26f6be2accc7d52bc38efff69f4" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-26T13:38:37.163599805" + }, + "mirna_quant_edger_qc": { + "content": [ + true, + true, + true, + true, + true, + true, + true, + true, + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-26T13:38:38.608879537" + }, + "fastqc_raw": { + "content": [ + true, + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-26T13:38:39.284103338" + }, + "multiqc_multiqc_data": { + "content": [ + "fastqc-status-check-heatmap.txt:md5,a16737b9ae7b9b70b0ef7e462101a729", + "fastqc_overrepresented_sequences_plot.txt:md5,0cacfefcbc37b292ae21564f845dfaa6", + "mirtrace_complexity_plot.txt:md5,8c3fae2d2b8fbbe922efd861b8675805", + "multiqc_citations.txt:md5,f46d2983044658a4a89bdec5ba20fda3", + true, + "fastqc_sequence_length_distribution_plot.txt:md5,ff2def0eab8321d4ed590b483641f43b", + true, + "fastqc_per_base_n_content_plot.txt:md5,c345fe5430e3a17ad1dbcc14e7595f50", + "fastqc_per_sequence_quality_scores_plot.txt:md5,edf4d21e2928d37d94bb33a25e1d92a6", + "mirtrace_qc_plot.txt:md5,82c1758d3f20a3e58eff3ebd456ee2f1", + "mirtrace_length_plot.txt:md5,69721d1a60f4a055da2bf091cedd48b3", + true, + "fastqc_sequence_counts_plot.txt:md5,da84941084250726e3828e8908640f8b", + "mirtrace_rna_categories_plot.txt:md5,bf50773cc4c0a82a0dd5b4fe91471062", + true, + "fastqc_per_base_sequence_quality_plot.txt:md5,60f539c88c503680c0b2603749494948", + true, + true, + true, + "fastqc_sequence_duplication_levels_plot.txt:md5,7e7eb4105b8f963bdf68e422e4ebce67", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,7ac995de6a861676f64879b02d04f819", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,c18bf431a08ec1230720d83781e8903b", + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-26T13:38:47.048873684" + }, + "mirna_quant_seqcluster": { + "content": [ + "small_Clone1_N3.fastp_trimmed.fastq.gz:md5,1bd799775d6913d60e51dcbf50c39c62", + "small_Clone1_N1.fastp_trimmed.fastq.gz:md5,21c736de10e306f14ec296eaeb38ef45" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-26T13:38:36.043210366" + }, + "mirtrace_qc_passed_reads.rnatype_unknown.collapsed": { + "content": [ + "small_Clone1_N3.fastp.fasta:md5,ca465c7e3c2aabe56f579fd01e091171", + "small_Clone1_N1.fastp.fasta:md5,293e3a6812111905c073f15fb0fa2169" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-26T13:38:42.273316368" + }, + "bowtie_index_mirna_mature": { + "content": [ + "fasta_bidx.2.ebwt:md5,778bd05aa462c2119736f9a4056bc41f", + "fasta_bidx.1.ebwt:md5,11a2f568aa785d32246cb8ce1aa8add4", + "fasta_bidx.4.ebwt:md5,78260e9dde22d8f31622c77d71bbb605", + "fasta_bidx.3.ebwt:md5,7aeccc6ec919ce1cfcd2b1e40be743fe", + "fasta_bidx.rev.2.ebwt:md5,ab52bc362b4c382cf213a71219e9efee", + "fasta_bidx.rev.1.ebwt:md5,0520d43b6b75328f3c30254a2d6baa18" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-26T13:38:45.344599116" + }, + "bowtie_index_mirna_hairpin": { + "content": [ + "fasta_bidx.3.ebwt:md5,5c60180e2f6fc2e0c399f10b9f9bbee2", + "fasta_bidx.2.ebwt:md5,6d99166d1a8a7a1bbf262e89db218278", + "fasta_bidx.1.ebwt:md5,40c2c142e094ab5ea531a0564ad62cee", + "fasta_bidx.rev.2.ebwt:md5,4270939b810aa3f461bacee1edc993aa", + "fasta_bidx.4.ebwt:md5,c3d4dbfbb587261ddf29e906029c10b1", + "fasta_bidx.rev.1.ebwt:md5,4532fb1426b29163b23702c8daf84d62" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-26T13:38:43.962724258" + }, + "mirtrace_qc_passed_reads.all.collapsed": { + "content": [ + "small_Clone1_N3.fastp.fasta:md5,c56851cf67339ed86f852a0f93bfe410", + "small_Clone1_N1.fastp.fasta:md5,980a9ce357496d7c12d598270ccfedcd" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-26T13:38:40.647810605" + }, + "mirna_quant_mirtop": { + "content": [ + true, + "mirtop_rawData.tsv:md5,847886d65be061e26b73aa42115c5be3", + true, + "mirna.tsv:md5,b26e9f5d7535104500e85673b97182a2", + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.10.0" + }, + "timestamp": "2024-08-26T13:38:37.883500873" + } +} \ No newline at end of file From e843703b0213541c52880e396d07e1fec1b2a1ef Mon Sep 17 00:00:00 2001 From: nschcolnicov Date: Mon, 26 Aug 2024 15:45:44 +0000 Subject: [PATCH 15/15] Updated snaps --- tests/test.nf.test.snap | 64 +++++++++++------------ tests/test_index.nf.test.snap | 64 +++++++++++------------ tests/test_no_genome.nf.test.snap | 64 +++++++++++------------ tests/test_technical_repeats.nf.test.snap | 44 ++++++++-------- tests/test_umi.nf.test.snap | 54 +++++++++---------- 5 files changed, 145 insertions(+), 145 deletions(-) diff --git a/tests/test.nf.test.snap b/tests/test.nf.test.snap index 43c24334..39ccd69f 100644 --- a/tests/test.nf.test.snap +++ b/tests/test.nf.test.snap @@ -34,19 +34,19 @@ }, "mirtrace": { "content": [ - "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", - "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", - "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", - "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", - "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", - "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", - "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638" + "mirtrace-stats-contamination_basic.tsv:md5,a67910702b13918a7d53f1283119f899", + "mirtrace-stats-length.tsv:md5,0609fcb0014f0d2af3308655b2418635", + "mirtrace-stats-contamination_detailed.tsv:md5,feb096d380e1ae62b4e73d54ed79e891", + "mirtrace-stats-rnatype.tsv:md5,8a333ff54c189c4a5a175a619139a9ac", + "mirtrace-stats-phred.tsv:md5,3f645df09c8eb314577cf6c4afda10f4", + "mirtrace-stats-qcstatus.tsv:md5,5fdd73860d2df454e21593df68975459", + "mirtrace-stats-mirna-complexity.tsv:md5,fce67408e9a9ab4a1a6f97e7e23ea2c8" ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T22:51:53.974696252" + "timestamp": "2024-08-26T14:47:45.013663624" }, "mirna_quant_reference": { "content": [ @@ -209,7 +209,7 @@ "fastqc_overrepresented_sequences_plot.txt:md5,d861a4a956a3023efa19b1259d8665b2", true, "fastqc_sequence_counts_plot-1.txt:md5,37d8ae6c5734eb2679e65e46c9af9101", - "mirtrace_complexity_plot.txt:md5,5f78d6f559a9642e68e1fd74ac2c11ca", + "mirtrace_complexity_plot.txt:md5,bb92ed0659dddb15d3e01686acef85b5", "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", true, @@ -222,14 +222,14 @@ "fastqc_per_base_n_content_plot.txt:md5,fb8a49467d1679dbf716e1f00c1f25e5", "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,b1481a9fbf5ea541b39aed99b51d616f", "fastqc_per_sequence_quality_scores_plot.txt:md5,38dbd6509de7f1beac17e44acb8336be", - "mirtrace_qc_plot.txt:md5,c436d017382baed6617fc3c1ad8ab41d", + "mirtrace_qc_plot.txt:md5,9036243402f6248214dc0458cb1291e9", "fastqc_per_sequence_quality_scores_plot-1.txt:md5,69f4459318311103fe71a5d1d3b2c076", - "mirtrace_length_plot.txt:md5,2366f10eb8bd3c32d2b35e2df20c786c", + "mirtrace_length_plot.txt:md5,86a0d54324cbe4817b112b02d4872cbb", true, "fastqc_overrepresented_sequences_plot-1.txt:md5,1de000de50cc7516bb9d996def14c6eb", "fastqc-status-check-heatmap-1.txt:md5,e64c353797e6dc057d10b3194ca6b20d", "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", - "mirtrace_rna_categories_plot.txt:md5,8665376e2a123e1661f82cbbee54789f", + "mirtrace_rna_categories_plot.txt:md5,9a57e6b3a3dd75906134030d25f6a7a9", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", true, "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", @@ -251,7 +251,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T22:52:27.886436979" + "timestamp": "2024-08-26T14:48:43.985133435" }, "mirna_quant_seqcluster": { "content": [ @@ -272,20 +272,20 @@ }, "mirtrace_qc_passed_reads.rnatype_unknown.collapsed": { "content": [ - "Clone1_N1.fastp.fasta:md5,e297dfa46353946d6c140e4513dd4525", - "Clone9_N1.fastp.fasta:md5,63a17d136548fc98f34c8d98006cc7da", - "Control_N3.fastp.fasta:md5,d9980a598ece252e19d6c9ebefd51861", - "Control_N1.fastp.fasta:md5,e964e05ce2c93937a8e76602f2e08150", - "Clone9_N2.fastp.fasta:md5,b1ca39e6e1e75ee7d654d9ccfb35e906", - "Control_N2.fastp.fasta:md5,8cefbc494be7b363b19c10b8c00366b2", - "Clone1_N3.fastp.fasta:md5,4012282462dde0750f09cec883304cc3", - "Clone9_N3.fastp.fasta:md5,f733e20eb8d2a2009ca82464e8ccb148" + "Clone1_N1.fastp.fasta:md5,ba5a705fbc7c4aadd259c29c3a443d97", + "Clone9_N1.fastp.fasta:md5,3e9a4ce784cbcdb946a3e271cc899da9", + "Control_N3.fastp.fasta:md5,850c3a525359f14ea488fcd0eedc2e36", + "Control_N1.fastp.fasta:md5,446f3452ffac337eb1afa5861c2ba94a", + "Clone9_N2.fastp.fasta:md5,168aa25977927be9480f9fe2399a82c7", + "Control_N2.fastp.fasta:md5,5018f8b15dbd524eb7dd0ce39e9b7101", + "Clone1_N3.fastp.fasta:md5,7a6c3163b377b25cf2886004ea9d4a73", + "Clone9_N3.fastp.fasta:md5,80a4b70ef276cf5628dfa2942c7e4988" ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T22:52:09.114139077" + "timestamp": "2024-08-26T14:48:32.628512644" }, "genome_quant_bam": { "content": [ @@ -368,20 +368,20 @@ }, "mirtrace_qc_passed_reads.all.collapsed": { "content": [ - "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", - "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", - "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", - "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", - "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", - "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", - "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", - "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8" + "Clone1_N1.fastp.fasta:md5,3761badda2e1c2dd2da3eb1bbfe6e1f8", + "Clone9_N1.fastp.fasta:md5,97310b5094e02329f412bae2657a2765", + "Control_N3.fastp.fasta:md5,f24ddebb1b012ec3817b88ff2e8989ea", + "Control_N1.fastp.fasta:md5,888c2e9639dd152d2f63e3c00019376b", + "Clone9_N2.fastp.fasta:md5,7f3879545cf3beb43af71ce83430abbf", + "Control_N2.fastp.fasta:md5,16e03efca3b17ec279658ad1556f52e4", + "Clone1_N3.fastp.fasta:md5,c6f029e821dceb6d60869a8f3e6e8198", + "Clone9_N3.fastp.fasta:md5,43d45f4416d0028f9adadd0f5ca44d9c" ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T22:51:59.69892856" + "timestamp": "2024-08-26T14:48:10.730193602" }, "mirna_quant_mirtop": { "content": [ @@ -397,4 +397,4 @@ }, "timestamp": "2024-08-22T22:51:32.899870265" } -} \ No newline at end of file +} diff --git a/tests/test_index.nf.test.snap b/tests/test_index.nf.test.snap index 2d35b6f4..323a9cdb 100644 --- a/tests/test_index.nf.test.snap +++ b/tests/test_index.nf.test.snap @@ -18,19 +18,19 @@ }, "mirtrace": { "content": [ - "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", - "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", - "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", - "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", - "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa", - "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", - "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638" + "mirtrace-stats-rnatype.tsv:md5,8a333ff54c189c4a5a175a619139a9ac", + "mirtrace-stats-length.tsv:md5,0609fcb0014f0d2af3308655b2418635", + "mirtrace-stats-contamination_basic.tsv:md5,a67910702b13918a7d53f1283119f899", + "mirtrace-stats-contamination_detailed.tsv:md5,feb096d380e1ae62b4e73d54ed79e891", + "mirtrace-stats-phred.tsv:md5,3f645df09c8eb314577cf6c4afda10f4", + "mirtrace-stats-qcstatus.tsv:md5,5fdd73860d2df454e21593df68975459", + "mirtrace-stats-mirna-complexity.tsv:md5,fce67408e9a9ab4a1a6f97e7e23ea2c8" ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T22:10:40.727064117" + "timestamp": "2024-08-26T14:59:18.343473208" }, "mirna_quant_reference": { "content": [ @@ -193,7 +193,7 @@ "fastqc_overrepresented_sequences_plot.txt:md5,d861a4a956a3023efa19b1259d8665b2", true, "fastqc_sequence_counts_plot-1.txt:md5,37d8ae6c5734eb2679e65e46c9af9101", - "mirtrace_complexity_plot.txt:md5,5f78d6f559a9642e68e1fd74ac2c11ca", + "mirtrace_complexity_plot.txt:md5,bb92ed0659dddb15d3e01686acef85b5", "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", true, @@ -206,14 +206,14 @@ "fastqc_per_base_n_content_plot.txt:md5,fb8a49467d1679dbf716e1f00c1f25e5", "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,b1481a9fbf5ea541b39aed99b51d616f", "fastqc_per_sequence_quality_scores_plot.txt:md5,38dbd6509de7f1beac17e44acb8336be", - "mirtrace_qc_plot.txt:md5,c436d017382baed6617fc3c1ad8ab41d", + "mirtrace_qc_plot.txt:md5,9036243402f6248214dc0458cb1291e9", "fastqc_per_sequence_quality_scores_plot-1.txt:md5,69f4459318311103fe71a5d1d3b2c076", - "mirtrace_length_plot.txt:md5,2366f10eb8bd3c32d2b35e2df20c786c", + "mirtrace_length_plot.txt:md5,86a0d54324cbe4817b112b02d4872cbb", true, "fastqc_overrepresented_sequences_plot-1.txt:md5,1de000de50cc7516bb9d996def14c6eb", "fastqc-status-check-heatmap-1.txt:md5,e64c353797e6dc057d10b3194ca6b20d", "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", - "mirtrace_rna_categories_plot.txt:md5,8665376e2a123e1661f82cbbee54789f", + "mirtrace_rna_categories_plot.txt:md5,9a57e6b3a3dd75906134030d25f6a7a9", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", true, "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", @@ -235,7 +235,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T22:11:37.214190607" + "timestamp": "2024-08-26T14:59:48.680287029" }, "untar_bowtie_index": { "content": [ @@ -271,20 +271,20 @@ }, "mirtrace_qc_passed_reads.rnatype_unknown.collapsed": { "content": [ - "Clone1_N1.fastp.fasta:md5,e297dfa46353946d6c140e4513dd4525", - "Clone9_N1.fastp.fasta:md5,63a17d136548fc98f34c8d98006cc7da", - "Control_N3.fastp.fasta:md5,d9980a598ece252e19d6c9ebefd51861", - "Control_N1.fastp.fasta:md5,e964e05ce2c93937a8e76602f2e08150", - "Clone9_N2.fastp.fasta:md5,b1ca39e6e1e75ee7d654d9ccfb35e906", - "Control_N2.fastp.fasta:md5,8cefbc494be7b363b19c10b8c00366b2", - "Clone1_N3.fastp.fasta:md5,4012282462dde0750f09cec883304cc3", - "Clone9_N3.fastp.fasta:md5,f733e20eb8d2a2009ca82464e8ccb148" + "Clone1_N1.fastp.fasta:md5,ba5a705fbc7c4aadd259c29c3a443d97", + "Clone9_N1.fastp.fasta:md5,3e9a4ce784cbcdb946a3e271cc899da9", + "Control_N3.fastp.fasta:md5,850c3a525359f14ea488fcd0eedc2e36", + "Control_N1.fastp.fasta:md5,446f3452ffac337eb1afa5861c2ba94a", + "Clone9_N2.fastp.fasta:md5,168aa25977927be9480f9fe2399a82c7", + "Control_N2.fastp.fasta:md5,5018f8b15dbd524eb7dd0ce39e9b7101", + "Clone1_N3.fastp.fasta:md5,7a6c3163b377b25cf2886004ea9d4a73", + "Clone9_N3.fastp.fasta:md5,80a4b70ef276cf5628dfa2942c7e4988" ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T22:10:57.082105969" + "timestamp": "2024-08-26T14:59:34.948240231" }, "bowtie_index_mirna_mature": { "content": [ @@ -318,20 +318,20 @@ }, "mirtrace_qc_passed_reads.all.collapsed": { "content": [ - "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", - "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", - "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", - "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", - "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", - "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", - "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", - "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8" + "Clone1_N1.fastp.fasta:md5,3761badda2e1c2dd2da3eb1bbfe6e1f8", + "Clone9_N1.fastp.fasta:md5,97310b5094e02329f412bae2657a2765", + "Control_N3.fastp.fasta:md5,f24ddebb1b012ec3817b88ff2e8989ea", + "Control_N1.fastp.fasta:md5,888c2e9639dd152d2f63e3c00019376b", + "Clone9_N2.fastp.fasta:md5,7f3879545cf3beb43af71ce83430abbf", + "Control_N2.fastp.fasta:md5,16e03efca3b17ec279658ad1556f52e4", + "Clone1_N3.fastp.fasta:md5,c6f029e821dceb6d60869a8f3e6e8198", + "Clone9_N3.fastp.fasta:md5,43d45f4416d0028f9adadd0f5ca44d9c" ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T22:10:45.973826356" + "timestamp": "2024-08-26T14:59:21.2869702" }, "mirna_quant_mirtop": { "content": [ @@ -347,4 +347,4 @@ }, "timestamp": "2024-08-22T22:10:16.715546319" } -} \ No newline at end of file +} diff --git a/tests/test_no_genome.nf.test.snap b/tests/test_no_genome.nf.test.snap index c9a5477e..1035e8fb 100644 --- a/tests/test_no_genome.nf.test.snap +++ b/tests/test_no_genome.nf.test.snap @@ -18,19 +18,19 @@ }, "mirtrace": { "content": [ - "mirtrace-stats-mirna-complexity.tsv:md5,6f7c2ced9fae8315b2ebb91dd6db9638", - "mirtrace-stats-length.tsv:md5,c09651fb8f8417aafad3f3173ae855df", - "mirtrace-stats-contamination_detailed.tsv:md5,3256b063ab94df31154104416abdeafe", - "mirtrace-stats-contamination_basic.tsv:md5,baeeda551a91def51b0d945b4c1ea8a2", - "mirtrace-stats-rnatype.tsv:md5,fdba5f1ccad362dfa2a2e219aa5b16e7", - "mirtrace-stats-qcstatus.tsv:md5,00a31eee51e4b2306e83fcdc65790da3", - "mirtrace-stats-phred.tsv:md5,4b8fa6f5aaeb4f2e43fcb1afa40ebcfa" + "mirtrace-stats-mirna-complexity.tsv:md5,fce67408e9a9ab4a1a6f97e7e23ea2c8", + "mirtrace-stats-length.tsv:md5,0609fcb0014f0d2af3308655b2418635", + "mirtrace-stats-contamination_detailed.tsv:md5,feb096d380e1ae62b4e73d54ed79e891", + "mirtrace-stats-contamination_basic.tsv:md5,a67910702b13918a7d53f1283119f899", + "mirtrace-stats-rnatype.tsv:md5,8a333ff54c189c4a5a175a619139a9ac", + "mirtrace-stats-qcstatus.tsv:md5,5fdd73860d2df454e21593df68975459", + "mirtrace-stats-phred.tsv:md5,3f645df09c8eb314577cf6c4afda10f4" ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T22:12:34.488403228" + "timestamp": "2024-08-26T15:19:07.296656154" }, "mirna_quant_reference": { "content": [ @@ -241,7 +241,7 @@ "fastqc_overrepresented_sequences_plot.txt:md5,d861a4a956a3023efa19b1259d8665b2", true, "fastqc_sequence_counts_plot-1.txt:md5,37d8ae6c5734eb2679e65e46c9af9101", - "mirtrace_complexity_plot.txt:md5,5f78d6f559a9642e68e1fd74ac2c11ca", + "mirtrace_complexity_plot.txt:md5,bb92ed0659dddb15d3e01686acef85b5", "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,edf5130b48b0814788867dd42e9cf407", "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", true, @@ -254,14 +254,14 @@ "fastqc_per_base_n_content_plot.txt:md5,fb8a49467d1679dbf716e1f00c1f25e5", "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,b1481a9fbf5ea541b39aed99b51d616f", "fastqc_per_sequence_quality_scores_plot.txt:md5,38dbd6509de7f1beac17e44acb8336be", - "mirtrace_qc_plot.txt:md5,c436d017382baed6617fc3c1ad8ab41d", + "mirtrace_qc_plot.txt:md5,9036243402f6248214dc0458cb1291e9", "fastqc_per_sequence_quality_scores_plot-1.txt:md5,69f4459318311103fe71a5d1d3b2c076", - "mirtrace_length_plot.txt:md5,2366f10eb8bd3c32d2b35e2df20c786c", + "mirtrace_length_plot.txt:md5,86a0d54324cbe4817b112b02d4872cbb", true, "fastqc_overrepresented_sequences_plot-1.txt:md5,1de000de50cc7516bb9d996def14c6eb", "fastqc-status-check-heatmap-1.txt:md5,e64c353797e6dc057d10b3194ca6b20d", "fastqc_sequence_counts_plot.txt:md5,384516be5885fdeac59e70c17f1413c2", - "mirtrace_rna_categories_plot.txt:md5,8665376e2a123e1661f82cbbee54789f", + "mirtrace_rna_categories_plot.txt:md5,9a57e6b3a3dd75906134030d25f6a7a9", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,65685440fcb927115ac30b01133e2f92", true, "fastqc_per_base_sequence_quality_plot.txt:md5,80ea53d94917cadcb41f3fdb56cba014", @@ -283,7 +283,7 @@ "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T22:15:02.747986455" + "timestamp": "2024-08-26T15:19:17.521099383" }, "mirna_quant_seqcluster": { "content": [ @@ -304,20 +304,20 @@ }, "mirtrace_qc_passed_reads.rnatype_unknown.collapsed": { "content": [ - "Clone1_N1.fastp.fasta:md5,e297dfa46353946d6c140e4513dd4525", - "Clone9_N1.fastp.fasta:md5,63a17d136548fc98f34c8d98006cc7da", - "Control_N3.fastp.fasta:md5,d9980a598ece252e19d6c9ebefd51861", - "Control_N1.fastp.fasta:md5,e964e05ce2c93937a8e76602f2e08150", - "Clone9_N2.fastp.fasta:md5,b1ca39e6e1e75ee7d654d9ccfb35e906", - "Control_N2.fastp.fasta:md5,8cefbc494be7b363b19c10b8c00366b2", - "Clone1_N3.fastp.fasta:md5,4012282462dde0750f09cec883304cc3", - "Clone9_N3.fastp.fasta:md5,f733e20eb8d2a2009ca82464e8ccb148" + "Clone1_N1.fastp.fasta:md5,ba5a705fbc7c4aadd259c29c3a443d97", + "Clone9_N1.fastp.fasta:md5,3e9a4ce784cbcdb946a3e271cc899da9", + "Control_N3.fastp.fasta:md5,850c3a525359f14ea488fcd0eedc2e36", + "Control_N1.fastp.fasta:md5,446f3452ffac337eb1afa5861c2ba94a", + "Clone9_N2.fastp.fasta:md5,168aa25977927be9480f9fe2399a82c7", + "Control_N2.fastp.fasta:md5,5018f8b15dbd524eb7dd0ce39e9b7101", + "Clone1_N3.fastp.fasta:md5,7a6c3163b377b25cf2886004ea9d4a73", + "Clone9_N3.fastp.fasta:md5,80a4b70ef276cf5628dfa2942c7e4988" ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T22:13:32.848948424" + "timestamp": "2024-08-26T15:19:14.421401668" }, "bowtie_index_mirna_mature": { "content": [ @@ -351,20 +351,20 @@ }, "mirtrace_qc_passed_reads.all.collapsed": { "content": [ - "Clone1_N1.fastp.fasta:md5,2b7ae92e9b8fcdfa34b62e39d13e49be", - "Clone9_N1.fastp.fasta:md5,c82f662747004a6873580898e29e1f44", - "Control_N3.fastp.fasta:md5,178c466a3dae3c168dc1bdaffa647e77", - "Control_N1.fastp.fasta:md5,5e377b864d5d4443234b46593884514c", - "Clone9_N2.fastp.fasta:md5,0a676933f44f59ccbf388093e1815b22", - "Control_N2.fastp.fasta:md5,8b11f194e66d35d8240cabf4493950ef", - "Clone1_N3.fastp.fasta:md5,b52ce91e385589c82474039c32b9bc0d", - "Clone9_N3.fastp.fasta:md5,d1b074453b3edb85ada10bd7d82b66a8" + "Clone1_N1.fastp.fasta:md5,3761badda2e1c2dd2da3eb1bbfe6e1f8", + "Clone9_N1.fastp.fasta:md5,97310b5094e02329f412bae2657a2765", + "Control_N3.fastp.fasta:md5,f24ddebb1b012ec3817b88ff2e8989ea", + "Control_N1.fastp.fasta:md5,888c2e9639dd152d2f63e3c00019376b", + "Clone9_N2.fastp.fasta:md5,7f3879545cf3beb43af71ce83430abbf", + "Control_N2.fastp.fasta:md5,16e03efca3b17ec279658ad1556f52e4", + "Clone1_N3.fastp.fasta:md5,c6f029e821dceb6d60869a8f3e6e8198", + "Clone9_N3.fastp.fasta:md5,43d45f4416d0028f9adadd0f5ca44d9c" ], "meta": { "nf-test": "0.9.0", "nextflow": "23.10.0" }, - "timestamp": "2024-08-22T22:12:47.213844865" + "timestamp": "2024-08-26T15:19:10.317601475" }, "mirna_quant_mirtop": { "content": [ @@ -380,4 +380,4 @@ }, "timestamp": "2024-08-22T22:12:05.154814163" } -} \ No newline at end of file +} diff --git a/tests/test_technical_repeats.nf.test.snap b/tests/test_technical_repeats.nf.test.snap index 6b04897b..7472e123 100644 --- a/tests/test_technical_repeats.nf.test.snap +++ b/tests/test_technical_repeats.nf.test.snap @@ -17,19 +17,19 @@ }, "mirtrace": { "content": [ - "mirtrace-stats-contamination_basic.tsv:md5,ca3f99b1b89d2674864b62bbf9c41592", - "mirtrace-stats-length.tsv:md5,71591c754eed9db419b91fb499f8e2ab", - "mirtrace-stats-qcstatus.tsv:md5,37465e5d4d756792b95f187e6406fc6b", - "mirtrace-stats-contamination_detailed.tsv:md5,c16e27cc433dacdd5bfff09a9aaab736", - "mirtrace-stats-phred.tsv:md5,1ac6fdae848cc4e39904edc361f75d1f", - "mirtrace-stats-mirna-complexity.tsv:md5,c69c4762a887a8e792c896dc5d3866b8", - "mirtrace-stats-rnatype.tsv:md5,2843855add34a73acd332a112bd80a34" + "mirtrace-stats-contamination_basic.tsv:md5,e27f51e118896c51ffcf4e6876da32c3", + "mirtrace-stats-length.tsv:md5,7b3a33f0237c050b43dff34b52edbbf2", + "mirtrace-stats-qcstatus.tsv:md5,9ebba807d2ef929bb0bd9029847571a8", + "mirtrace-stats-contamination_detailed.tsv:md5,2f3b3fd832e8c09fc4be81957b259e31", + "mirtrace-stats-phred.tsv:md5,e2cedb9d91521823c648365dd6606f4a", + "mirtrace-stats-mirna-complexity.tsv:md5,39d7405425c3db8faa3514fb33a81492", + "mirtrace-stats-rnatype.tsv:md5,b2a56404c01c0b44b20a03c50285cc2d" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nf-test": "0.8.4", + "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T22:46:28.913796722" + "timestamp": "2024-08-26T15:36:54.667308127" }, "mirna_quant_reference": { "content": [ @@ -132,15 +132,15 @@ }, "mirtrace_qc_passed_reads.rnatype_unknown.collapsed": { "content": [ - "Clone1_N1.fastp.fasta:md5,f49d63f3d05aeb349f58f2bb95552332", - "Control_N1.fastp.fasta:md5,b34c20e0736351db5d0d1d3236de18ec", - "Clone9_N3.fastp.fasta:md5,726d1d14a88d7b816bb97bab9f006c45" + "Clone1_N1.fastp.fasta:md5,869717d19534f6f89aa43bcad6256603", + "Control_N1.fastp.fasta:md5,35910fa3cfd3956634f562d31dfc92b1", + "Clone9_N3.fastp.fasta:md5,9c00a9ad6365891b828f381baf600c31" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nf-test": "0.8.4", + "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T22:46:32.009856508" + "timestamp": "2024-08-26T15:36:55.12102921" }, "genome_quant_bam": { "content": [ @@ -198,15 +198,15 @@ }, "mirtrace_qc_passed_reads.all.collapsed": { "content": [ - "Clone1_N1.fastp.fasta:md5,7630d5d8f047d2f7e9492598e6f97c84", - "Control_N1.fastp.fasta:md5,534de89c8354a874458497804dcb7785", - "Clone9_N3.fastp.fasta:md5,0f2ef6c209a0b591d4eff5d77b713957" + "Clone1_N1.fastp.fasta:md5,1c1c8ceb14bafb43548abca69e61ffa0", + "Control_N1.fastp.fasta:md5,643d639fc1a56f2fa7616a1ba8b8dd22", + "Clone9_N3.fastp.fasta:md5,b0d3a983db699e9c429012a02de33268" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nf-test": "0.8.4", + "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T22:46:36.356862083" + "timestamp": "2024-08-26T15:36:56.134008484" }, "mirna_quant_mirtop": { "content": [ diff --git a/tests/test_umi.nf.test.snap b/tests/test_umi.nf.test.snap index 64e295ac..df5aaa96 100644 --- a/tests/test_umi.nf.test.snap +++ b/tests/test_umi.nf.test.snap @@ -28,19 +28,19 @@ }, "mirtrace": { "content": [ - "mirtrace-stats-contamination_detailed.tsv:md5,428d2fd6ea0a6f2af1018a557e89bece", - "mirtrace-stats-mirna-complexity.tsv:md5,cd2f37963adeee159764a89688a4a6a5", - "mirtrace-stats-length.tsv:md5,3edbc31452dba97f8b829e3f8f635955", - "mirtrace-stats-contamination_basic.tsv:md5,3d54b37ab3206e9fec909fe3ea1a4777", - "mirtrace-stats-qcstatus.tsv:md5,de4f8a670b736bedf348d358cfdfb9fc", + "mirtrace-stats-contamination_detailed.tsv:md5,4015530b4d5935b241eb70bf0c51dfad", + "mirtrace-stats-mirna-complexity.tsv:md5,9ed7b0c56b5fe2913cadf9a47f2d4731", + "mirtrace-stats-length.tsv:md5,b9f57e2e6c950a065a28769928d7dbdd", + "mirtrace-stats-contamination_basic.tsv:md5,cf6ced069895d8d6183a5b391c532d1c", + "mirtrace-stats-qcstatus.tsv:md5,bc24cec6cfa63462005d86dba95cfdfd", "mirtrace-stats-phred.tsv:md5,8cf9fc2223b9aeb50f92c8845edbf535", - "mirtrace-stats-rnatype.tsv:md5,00e584439bec82f5de8d6485a73dec37" + "mirtrace-stats-rnatype.tsv:md5,b485dc91adfc66a2237f145430dfbc21" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nf-test": "0.8.4", + "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T22:52:15.212444825" + "timestamp": "2024-08-26T15:42:33.712941492" }, "mirna_quant_reference": { "content": [ @@ -153,7 +153,7 @@ "fastp_filtered_reads_plot.txt:md5,3aaa79e1ede44347971c26100d9e954b", true, "fastqc_sequence_counts_plot-1.txt:md5,24744e039ce4dbcbacf42edbfd642a8b", - "mirtrace_complexity_plot.txt:md5,5a860a872f793250b8c4482d031176a8", + "mirtrace_complexity_plot.txt:md5,03b2a5783383193eeee4a3a094612112", "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,351f949c0abf4fb7587f3f5d9a28d461", "multiqc_citations.txt:md5,3adbccd17a42d0d5d97ee7ebb476f433", true, @@ -166,13 +166,13 @@ "fastqc_per_base_n_content_plot.txt:md5,5b5b8cee3162d092c0bcddffbd000f34", "fastp-seq-quality-plot_Read_1_After_filtering.txt:md5,66a47c7ce00ede2053f8e6eb20ec3417", "fastqc_per_sequence_quality_scores_plot.txt:md5,3aa99649540afc898d32d2e49a364487", - "mirtrace_qc_plot.txt:md5,b08d11ea51c54e615f9608002644c787", + "mirtrace_qc_plot.txt:md5,b8e9e241fd258a3ddd13ae407d6dd746", "fastqc_per_sequence_quality_scores_plot-1.txt:md5,4108da6fe352558a652ee2b17d609e07", - "mirtrace_length_plot.txt:md5,440a84ce9bbdb89b736e4e2446382665", + "mirtrace_length_plot.txt:md5,3f84d4b3dd20053815b7524bc43f0261", true, "fastqc-status-check-heatmap-1.txt:md5,cb2ea844834808ae4c95c6440269cf2e", "fastqc_sequence_counts_plot.txt:md5,5e5c5132ff1969dfa40cb8b1eadf7a46", - "mirtrace_rna_categories_plot.txt:md5,6d08c297377a6241c4c1e82278d71f32", + "mirtrace_rna_categories_plot.txt:md5,d7d616cd1ef0797727299f8820f50ab9", "fastp-seq-quality-plot_Read_1_Before_filtering.txt:md5,f36b7cfd3057b26281367397db45033a", true, "fastqc_per_base_sequence_quality_plot.txt:md5,e2e187bc0b0c1f0d1abb3b666945c7b3", @@ -180,7 +180,7 @@ "fastp-seq-content-n-plot_Read_1_After_filtering.txt:md5,bbad2035ada86867c4ed579a93b78d64", true, true, - "mirtrace_contamination_check_plot.txt:md5,7f12917ce506127a729edb733fdda511", + "mirtrace_contamination_check_plot.txt:md5,46c2709ae5228d93ff117b88f9792620", "fastqc_adapter_content_plot.txt:md5,de1d7324ff5146b49fc9a2e6d4633962", "fastqc_sequence_duplication_levels_plot.txt:md5,fe7598e49f93bb980a7675a2bb4bd3b5", "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,c2f2f9282a50c3eef475664cc969b8ec", @@ -192,10 +192,10 @@ "fastp-seq-content-gc-plot_Read_1_After_filtering.txt:md5,d673e3b18c40c5af1edccffba386d678" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nf-test": "0.8.4", + "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T22:52:47.905877394" + "timestamp": "2024-08-26T15:42:34.218114878" }, "mirna_quant_seqcluster": { "content": [ @@ -210,14 +210,14 @@ }, "mirtrace_qc_passed_reads.rnatype_unknown.collapsed": { "content": [ - "SRX8195118_SRR11631014.fastp.fasta:md5,7db07b8c0b9e2b484eb3d42a04e480d1", - "SRX8195117_SRR11631013.fastp.fasta:md5,eb1ba9fa6f7d956e5d650fdd306d5634" + "SRX8195118_SRR11631014.fastp.fasta:md5,5aff6ac8bf0f5637b730ad8f49ac7a47", + "SRX8195117_SRR11631013.fastp.fasta:md5,08902643a45e944be04ad62dd4eaa610" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nf-test": "0.8.4", + "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T22:52:32.630636315" + "timestamp": "2024-08-26T15:42:34.012175996" }, "genome_quant_bam": { "content": [ @@ -281,14 +281,14 @@ }, "mirtrace_qc_passed_reads.all.collapsed": { "content": [ - "SRX8195118_SRR11631014.fastp.fasta:md5,99e2ce92ce102bd3fedc3a9d3b926873", - "SRX8195117_SRR11631013.fastp.fasta:md5,e0e31d882568a7853dea75b3c595108f" + "SRX8195118_SRR11631014.fastp.fasta:md5,472b73017f8a22c10855fd196f19c1c7", + "SRX8195117_SRR11631013.fastp.fasta:md5,d05deb2132050f04843341d613cc6e65" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "23.10.0" + "nf-test": "0.8.4", + "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T22:52:22.862929991" + "timestamp": "2024-08-26T15:42:33.842847298" }, "mirna_quant_mirtop": { "content": [