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Merge pull request #386 from nf-core/trim3p_nextflex
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,36 @@ | ||
| /* | ||
| ======================================================================================== | ||
| Nextflow config file for running minimal tests | ||
| ======================================================================================== | ||
| Defines input files and everything required to run a fast and simple pipeline test. | ||
| Use as follows: | ||
| nextflow run nf-core/smrnaseq -profile test_nextflex,<docker/singularity> | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
| // This test profile tests nextflex without genome | ||
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| params { | ||
| config_profile_name = 'Nextflex Test profile' | ||
| config_profile_description = 'Minimal test dataset to check pipeline function' | ||
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| // Limit resources so that this can run on GitHub Actions | ||
| max_cpus = 2 | ||
| max_memory = '6.GB' | ||
| max_time = '6.h' | ||
|
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| // Input data | ||
| input = 'https://raw.githubusercontent.com/nf-core/test-datasets/smrnaseq/samplesheet/v2.0/samplesheet_test_nextflex.csv' | ||
| mature = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/mature.fa' | ||
| hairpin = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/hairpin.fa' | ||
| mirna_gtf = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/hsa.gff3' | ||
| mirtrace_species = 'hsa' | ||
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| skip_mirdeep = true | ||
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| } | ||
|
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| // Include nextflex config to run test without additional profiles | ||
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| includeConfig 'protocol_nextflex.config' |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,122 @@ | ||
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| nextflow_pipeline { | ||
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| name "Test Workflow main.nf - test_nextflex" | ||
| script "main.nf" | ||
| profile "test_nextflex" | ||
| tag "test_nextflex" | ||
| tag "pipeline" | ||
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| test("test_nextflex") { | ||
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| when { | ||
| params { | ||
| outdir = "$outputDir" | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot(UTILS.removeNextflowVersion("$outputDir")).match("software_versions") }, | ||
| { assert workflow.trace.succeeded().size() == 65 }, | ||
|
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| { assert snapshot( | ||
| path("$outputDir/mirna_quant/bam/mature/sample2_mature.sorted.idxstats"), | ||
| path("$outputDir/mirna_quant/bam/mature/sample1_mature.sorted.flagstat"), | ||
| path("$outputDir/mirna_quant/bam/mature/sample2_mature.sorted.stats"), | ||
| path("$outputDir/mirna_quant/bam/mature/sample3_mature.sorted.stats"), | ||
| path("$outputDir/mirna_quant/bam/mature/sample3_mature.sorted.flagstat"), | ||
| path("$outputDir/mirna_quant/bam/mature/sample3_mature.sorted.idxstats"), | ||
| path("$outputDir/mirna_quant/bam/mature/sample1_mature.sorted.stats"), | ||
| path("$outputDir/mirna_quant/bam/mature/sample2_mature.sorted.flagstat"), | ||
| path("$outputDir/mirna_quant/bam/mature/sample1_mature.sorted.idxstats"), | ||
| path("$outputDir/mirna_quant/bam/hairpin/sample3_mature_hairpin.sorted.stats"), | ||
| path("$outputDir/mirna_quant/bam/hairpin/sample2_mature_hairpin.sorted.flagstat"), | ||
| path("$outputDir/mirna_quant/bam/hairpin/sample1_mature_hairpin.sorted.flagstat"), | ||
| path("$outputDir/mirna_quant/bam/hairpin/sample1_mature_hairpin.sorted.idxstats"), | ||
| path("$outputDir/mirna_quant/bam/hairpin/sample3_mature_hairpin.sorted.flagstat"), | ||
| path("$outputDir/mirna_quant/bam/hairpin/sample2_mature_hairpin.sorted.stats"), | ||
| path("$outputDir/mirna_quant/bam/hairpin/sample1_mature_hairpin.sorted.stats"), | ||
| path("$outputDir/mirna_quant/bam/hairpin/sample3_mature_hairpin.sorted.idxstats"), | ||
| path("$outputDir/mirna_quant/bam/hairpin/sample2_mature_hairpin.sorted.idxstats") | ||
| ).match("mirna_quant_bam") }, | ||
|
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||
| { assert snapshot( | ||
| path("$outputDir/mirna_quant/edger_qc/hairpin_counts.csv").exists(), | ||
| path("$outputDir/mirna_quant/edger_qc/hairpin_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/hairpin_log2CPM_sample_distances.txt").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("$outputDir/mirna_quant/edger_qc/mature_edgeR_MDS_distance_matrix.txt").exists(), | ||
| path("$outputDir/mirna_quant/edger_qc/mature_counts.csv").exists(), | ||
| path("$outputDir/mirna_quant/edger_qc/mature_log2CPM_sample_distances.txt").exists(), | ||
| path("$outputDir/mirna_quant/edger_qc/hairpin_unmapped_read_counts.txt").exists(), | ||
| path("$outputDir/mirna_quant/edger_qc/mature_normalized_CPM.txt").exists(), | ||
| path("$outputDir/mirna_quant/edger_qc/mature_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() | ||
| ).match("mirna_quant_edger_qc") }, | ||
|
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||
| { assert snapshot( | ||
| path("$outputDir/mirtrace/mirtrace-report.html").exists(), | ||
| path("$outputDir/mirtrace/mirtrace-stats-contamination_basic.tsv"), | ||
| path("$outputDir/mirtrace/mirtrace-stats-mirna-complexity.tsv"), | ||
| path("$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-rnatype.tsv") | ||
| ).match("mirtrace") }, | ||
|
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||
| { 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"), | ||
| 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("$outputDir/multiqc/multiqc_data/fastp-seq-content-n-plot_Read_1_After_filtering.txt"), | ||
| path("$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").exists(), | ||
| path("$outputDir/multiqc/multiqc_data/fastp-seq-content-gc-plot_Read_1_After_filtering.txt") | ||
| ).match("multiqc_multiqc_data") }, | ||
|
|
||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
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