From e7ae4f8447158990e09c0971d068f46fb88ffd58 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 3 May 2024 18:29:25 +0200 Subject: [PATCH 1/2] fix(tests): remove md5sum for all mosdepth tests + update dependency for these tests --- CHANGELOG.md | 2 + tests/config/pytesttags.yml | 23 +++++++ tests/test_aligner_bwamem.yml | 10 --- tests/test_aligner_bwamem2.yml | 10 --- tests/test_aligner_dragmap.yml | 10 --- tests/test_alignment_to_fastq.yml | 10 --- tests/test_cnvkit.yml | 30 -------- tests/test_controlfreec.yml | 23 ------- tests/test_deepvariant.yml | 9 --- tests/test_default.yml | 10 --- tests/test_fastp.yml | 20 ------ tests/test_freebayes.yml | 68 ------------------- tests/test_gatk4spark.yml | 20 ------ tests/test_haplotypecaller.yml | 9 --- tests/test_haplotypecaller_skip_filter.yml | 9 --- tests/test_intervals.yml | 32 --------- tests/test_joint_germline.yml | 30 -------- tests/test_manta.yml | 36 ---------- tests/test_markduplicates_from_bam.yml | 20 ------ tests/test_markduplicates_from_cram.yml | 20 ------ tests/test_mpileup.yml | 18 ----- tests/test_msisensorpro.yml | 10 --- tests/test_mutect2.yml | 9 --- tests/test_prepare_recalibration_from_bam.yml | 6 -- .../test_prepare_recalibration_from_cram.yml | 9 --- tests/test_recalibrate_from_bam.yml | 9 --- tests/test_recalibrate_from_cram.yml | 9 --- tests/test_save_mapped.yml | 10 --- tests/test_save_output_as_bam_only.yml | 10 --- tests/test_sentieon_aligner_bwamem.yml | 30 -------- tests/test_sentieon_dedup_from_bam.yml | 10 --- tests/test_sentieon_dedup_from_cram.yml | 10 --- tests/test_sentieon_dnascope.yml | 19 ------ tests/test_sentieon_dnascope_skip_filter.yml | 9 --- tests/test_sentieon_haplotyper.yml | 19 ------ ...est_sentieon_haplotyper_joint_germline.yml | 30 -------- .../test_sentieon_haplotyper_skip_filter.yml | 6 -- tests/test_skip_markduplicates.yml | 30 -------- tests/test_strelka.yml | 56 --------------- tests/test_strelka_bp.yml | 18 ----- tests/test_tiddit.yml | 20 ------ tests/test_tools_manually.yml | 48 ------------- tests/test_tumor_normal_pair.yml | 20 ------ tests/test_umi.yml | 10 --- 44 files changed, 25 insertions(+), 801 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index da6cf18dbb..ee79107fe7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,6 +26,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1488](https://github.com/nf-core/sarek/pull/1488) - Fixing call to `GATK4_HAPLOTYPECALLER` and thereby also the test-profile `test_full_germline` - [#1494](https://github.com/nf-core/sarek/pull/1494) - Fix Cloud Storage objects are immutable on GCP [#1491](https://github.com/nf-core/sarek/issues/1491) - [#1496](https://github.com/nf-core/sarek/pull/1496) - Fix multiple DOI handling in manifest +- [#1499](https://github.com/nf-core/sarek/pull/1499) - Remove all md5sum for mosdepth tests +- [#1499](https://github.com/nf-core/sarek/pull/1499) - Add mosdepth dependency to all tests runnning it ### Removed diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml index 0c3c05c554..ac74cb8931 100644 --- a/tests/config/pytesttags.yml +++ b/tests/config/pytesttags.yml @@ -76,6 +76,7 @@ validation_checks: alignment_to_fastq: - conf/modules/alignment_to_fastq.config - modules/nf-core/cat/fastq/** + - modules/nf-core/mosdepth/** - modules/nf-core/samtools/collatefastq/** - modules/nf-core/samtools/merge/** - modules/nf-core/samtools/view/** @@ -92,6 +93,7 @@ umi: - modules/nf-core/fgbio/callmolecularconsensusreads/** - modules/nf-core/fgbio/fastqtobam/** - modules/nf-core/fgbio/groupreadsbyumi/** + - modules/nf-core/mosdepth/** - modules/nf-core/samblaster/** - modules/nf-core/samtools/bam2fq/** - subworkflows/local/fastq_align_bwamem_mem2_dragmap/** @@ -103,6 +105,7 @@ umi: fastp: - conf/modules/trimming.config - modules/nf-core/fastp/** + - modules/nf-core/mosdepth/** - tests/csv/3.0/fastq_single.csv - tests/test_fastp.yml @@ -112,6 +115,7 @@ fastp: bwamem: - conf/modules/aligner.config - modules/nf-core/bwa/mem/** + - modules/nf-core/mosdepth/** - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/** - tests/csv/3.0/fastq_single.csv - tests/test_aligner_bwamem.yml @@ -120,6 +124,7 @@ bwamem: bwamem2: - conf/modules/aligner.config - modules/nf-core/bwamem2/mem/** + - modules/nf-core/mosdepth/** - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/** - tests/csv/3.0/fastq_single.csv - tests/test_aligner_bwamem2.yml @@ -128,6 +133,7 @@ bwamem2: dragmap: - conf/modules/aligner.config - modules/nf-core/dragmap/align/** + - modules/nf-core/mosdepth/** - subworkflows/local/fastq_align_bwamem_mem2_dragmap_sentieon/** - tests/csv/3.0/fastq_single.csv - tests/test_aligner_dragmap.yml @@ -174,6 +180,7 @@ prepare_recalibration: - conf/modules/prepare_recalibration.config - modules/nf-core/gatk4/baserecalibrator/** - modules/nf-core/gatk4/gatherbqsrreports/** + - modules/nf-core/mosdepth/** - modules/nf-core/samtools/convert/** - subworkflows/local/bam_baserecalibrator/** - tests/csv/3.0/mapped_single_bam.csv @@ -188,6 +195,7 @@ recalibrate: - modules/nf-core/samtools/convert/** - modules/nf-core/samtools/index/** - modules/nf-core/samtools/merge/** + - modules/nf-core/mosdepth/** - subworkflows/local/bam_applybqsr/** - subworkflows/local/cram_merge_index_samtools/** - tests/csv/3.0/prepare_recalibration_single_bam.csv @@ -201,6 +209,7 @@ intervals: - modules/local/build_intervals/** - modules/local/create_intervals_bed/** - modules/nf-core/gatk4/intervallisttobed/** + - modules/nf-core/mosdepth/** - modules/nf-core/tabix/bgziptabix/** - subworkflows/local/prepare_intervals/** - tests/csv/3.0/fastq_single.csv @@ -215,6 +224,7 @@ gatk4spark: - modules/nf-core/gatk4spark/baserecalibrator/** - modules/nf-core/gatk4/estimatelibrarycomplexity/** - modules/nf-core/gatk4spark/markduplicates/** + - modules/nf-core/mosdepth/** - subworkflows/local/bam_applybqsr_spark/** - subworkflows/local/bam_baserecalibrator_spark/** - subworkflows/local/bam_markduplicates_spark/** @@ -229,6 +239,7 @@ cnvkit: - modules/nf-core/cnvkit/antitarget/** - modules/nf-core/cnvkit/batch/** - modules/nf-core/cnvkit/reference/** + - modules/nf-core/mosdepth/** - subworkflows/local/bam_variant_calling_cnvkit/** - subworkflows/local/bam_variant_calling_germline_all/** - subworkflows/local/bam_variant_calling_somatic_all/** @@ -249,6 +260,7 @@ controlfreec: - modules/nf-core/controlfreec/freec2bed/** - modules/nf-core/controlfreec/freec2circos/** - modules/nf-core/controlfreec/makegraph2/** + - modules/nf-core/mosdepth/** - modules/nf-core/samtools/mpileup/** - subworkflows/local/bam_variant_calling_mpileup/** - subworkflows/local/bam_variant_calling_somatic_all/** @@ -264,6 +276,7 @@ deepvariant: - conf/modules/deepvariant.config - modules/nf-core/deepvariant/** - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/mosdepth/** - modules/nf-core/tabix/tabix/** - subworkflows/local/bam_variant_calling_deepvariant/** - subworkflows/local/bam_variant_calling_germline_all/** @@ -276,6 +289,7 @@ freebayes: - modules/nf-core/bcftools/sort/** - modules/nf-core/freebayes/** - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/mosdepth/** - modules/nf-core/tabix/tabix/** - subworkflows/local/bam_variant_calling_freebayes/** - subworkflows/local/bam_variant_calling_germline_all/** @@ -293,6 +307,7 @@ haplotypecaller: - modules/nf-core/gatk4/filtervarianttranches/** - modules/nf-core/gatk4/haplotypecaller/** - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/mosdepth/** - modules/nf-core/samtools/index/** - modules/nf-core/samtools/merge/** - subworkflows/local/bam_merge_index_samtools/** @@ -379,6 +394,7 @@ joint_germline: - modules/nf-core/gatk4/haplotypecaller/** - modules/nf-core/gatk4/mergevcfs/** - modules/nf-core/gatk4/variantrecalibrator/** + - modules/nf-core/mosdepth/** - modules/nf-core/samtools/index/** - modules/nf-core/samtools/merge/** - subworkflows/local/bam_joint_calling_germline_gatk/** @@ -418,6 +434,7 @@ manta: - modules/nf-core/manta/germline/** - modules/nf-core/manta/somatic/** - modules/nf-core/manta/tumoronly/** + - modules/nf-core/mosdepth/** - subworkflows/local/bam_variant_calling_germline_all/** - subworkflows/local/bam_variant_calling_germline_manta/** - subworkflows/local/bam_variant_calling_somatic_all/** @@ -433,6 +450,7 @@ manta: mpileup: - conf/modules/mpileup.config - modules/nf-core/cat/cat/** + - modules/nf-core/mosdepth/** - modules/nf-core/samtools/mpileup/** - subworkflows/local/bam_variant_calling_germline_all/** - subworkflows/local/bam_variant_calling_mpileup/** @@ -447,6 +465,7 @@ msisensorpro: - conf/modules/msisensorpro.config - modules/nf-core/msisensorpro/msi_somatic/** - modules/nf-core/msisensorpro/scan/** + - modules/nf-core/mosdepth/** - subworkflows/local/bam_variant_calling_somatic_all/** - tests/csv/3.0/recalibrated_somatic.csv - tests/test_msisensorpro.yml @@ -462,6 +481,7 @@ mutect2: - modules/nf-core/gatk4/mergemutectstats/** - modules/nf-core/gatk4/mergevcfs/** - modules/nf-core/gatk4/mutect2/** + - modules/nf-core/mosdepth/** - subworkflows/local/bam_variant_calling_somatic_all/** - subworkflows/local/bam_variant_calling_somatic_mutect2/** - subworkflows/local/bam_variant_calling_tumor_only_all/** @@ -473,6 +493,7 @@ mutect2: strelka: - conf/modules/strelka.config - modules/nf-core/gatk4/mergevcfs/** + - modules/nf-core/mosdepth/** - modules/nf-core/strelka/germline/** - modules/nf-core/strelka/somatic/** - subworkflows/local/bam_variant_calling_germline_all/** @@ -492,6 +513,7 @@ strelka_bp: - conf/modules/strelka.config - modules/nf-core/gatk4/mergevcfs/** - modules/nf-core/manta/somatic/** + - modules/nf-core/mosdepth/** - modules/nf-core/strelka/somatic/** - subworkflows/local/bam_variant_calling_germline_all/** - subworkflows/local/bam_variant_calling_somatic_all/** @@ -505,6 +527,7 @@ strelka_bp: tiddit: - conf/modules/tiddit.config - modules/nf-core/svdb/merge/**.nf + - modules/nf-core/mosdepth/** - modules/nf-core/tabix/bgziptabix/** - modules/nf-core/tiddit/sv/** - subworkflows/local/bam_variant_calling_germline_all/** diff --git a/tests/test_aligner_bwamem.yml b/tests/test_aligner_bwamem.yml index 372911cb81..ccd81021ef 100644 --- a/tests/test_aligner_bwamem.yml +++ b/tests/test_aligner_bwamem.yml @@ -42,25 +42,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_aligner_bwamem2.yml b/tests/test_aligner_bwamem2.yml index 7b870a7d99..be19c08df6 100644 --- a/tests/test_aligner_bwamem2.yml +++ b/tests/test_aligner_bwamem2.yml @@ -42,25 +42,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_aligner_dragmap.yml b/tests/test_aligner_dragmap.yml index 4aabdf592a..6f38538926 100644 --- a/tests/test_aligner_dragmap.yml +++ b/tests/test_aligner_dragmap.yml @@ -55,25 +55,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["LB0 27214 1086 322 1037558 20017 100 0 0.687981"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b0d7d5de1e00132bb5b47e1b3d90d944 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 02b88d7ec0ca8ff23ba688c35939fa05 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 1792d98676f597f755749f4286c5102d - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 590119568d091ce3a88f7fe4f43f24ff - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 2e7fe057ead0622e6a2a6b0ed1832315 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b0d7d5de1e00132bb5b47e1b3d90d944 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 02b88d7ec0ca8ff23ba688c35939fa05 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 1792d98676f597f755749f4286c5102d - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 590119568d091ce3a88f7fe4f43f24ff - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 2e7fe057ead0622e6a2a6b0ed1832315 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_alignment_to_fastq.yml b/tests/test_alignment_to_fastq.yml index 1b64f422e8..bc7a3e5057 100644 --- a/tests/test_alignment_to_fastq.yml +++ b/tests/test_alignment_to_fastq.yml @@ -25,25 +25,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986 1178 1178", "2.0 1.47674 800 800", "100.0 1.911145 0 0"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 9cb9b181119256ed17a77dcf44d58285 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: dbe376360e437c89190139ef0ae6769a - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: d9b53915d473710ff0260a0ff694fd32 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: d0713716f63ac573f4a3385733e9a537 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 9cb9b181119256ed17a77dcf44d58285 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: dbe376360e437c89190139ef0ae6769a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d9b53915d473710ff0260a0ff694fd32 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: d0713716f63ac573f4a3385733e9a537 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_cnvkit.yml b/tests/test_cnvkit.yml index 87adbc33c6..43828e540e 100644 --- a/tests/test_cnvkit.yml +++ b/tests/test_cnvkit.yml @@ -58,27 +58,17 @@ - path: results/cnvkit should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on tumor_only sample with cnvkit @@ -113,15 +103,10 @@ - path: results/cnvkit should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on germline sample with cnvkit command: nextflow run main.nf -profile test,tools_germline --tools cnvkit --outdir results @@ -157,15 +142,10 @@ - path: results/cnvkit should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal command: nextflow run main.nf -profile test,tools_somatic --tools cnvkit --only_paired_variant_calling --outdir results @@ -203,26 +183,16 @@ - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn md5sum: b4a49faf170e436ec32dcc21ccc3ce8f - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test diff --git a/tests/test_controlfreec.yml b/tests/test_controlfreec.yml index c3353561a0..d72b67ed27 100644 --- a/tests/test_controlfreec.yml +++ b/tests/test_controlfreec.yml @@ -51,27 +51,17 @@ - path: results/cnvkit should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic samples with controlfreec without intervals @@ -127,23 +117,15 @@ - path: results/mpileup should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.global.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/sample3/sample3.recal.summary.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz - md5sum: 1a60c330fb42841e8dcf3cd507a70bfc - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.global.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/sample4/sample4.recal.summary.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz - md5sum: 1a60c330fb42841e8dcf3cd507a70bfc - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on tumor_only sample with controlfreec @@ -190,13 +172,8 @@ - path: results/mpileup should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.global.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/sample2/sample2.recal.region.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/sample2/sample2.recal.summary.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 1a60c330fb42841e8dcf3cd507a70bfc - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/samtools/sample2/sample2.recal.cram.stats diff --git a/tests/test_deepvariant.yml b/tests/test_deepvariant.yml index 42660bd78a..d66f2e1aef 100644 --- a/tests/test_deepvariant.yml +++ b/tests/test_deepvariant.yml @@ -25,15 +25,10 @@ - path: results/deepvariant should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on germline sample with deepvariant without intervals command: nextflow run main.nf -profile test,tools_germline --tools deepvariant --no_intervals --outdir results @@ -69,11 +64,7 @@ - path: results/deepvariant should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample1/sample1.recal.cram.stats diff --git a/tests/test_default.yml b/tests/test_default.yml index 84f14e05f2..97ebb3918d 100644 --- a/tests/test_default.yml +++ b/tests/test_default.yml @@ -30,25 +30,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_fastp.yml b/tests/test_fastp.yml index e8fe306468..20eab4065f 100644 --- a/tests/test_fastp.yml +++ b/tests/test_fastp.yml @@ -31,25 +31,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 16608 1860 160 1046616 12117 256 0 0.621261"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 3098d33090a0f90f6fc16d497d2ce644 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 057a02943301a5acec55d19a5a629f11 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: fef22f026f7b4a89ab60c715689c5591 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: cca0f725bea04688b39f2ea8ad2e1605 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: a5ad8f917979f62eacfff1461529dbaa - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 3098d33090a0f90f6fc16d497d2ce644 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 057a02943301a5acec55d19a5a629f11 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: fef22f026f7b4a89ab60c715689c5591 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: cca0f725bea04688b39f2ea8ad2e1605 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: a5ad8f917979f62eacfff1461529dbaa - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -90,25 +80,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17482 890 170 1047682 12552 69 0 0.65881"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 3626e543b91aa564f0056747827366d3 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: e3442f1098899a22748d07ef436925f6 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 2873e7f9c9aede39942731894a6077d1 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 948108074663677f9225fd0574658ca1 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: d5f1c9389ecf52ba839e834780a94549 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 3626e543b91aa564f0056747827366d3 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: e3442f1098899a22748d07ef436925f6 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 2873e7f9c9aede39942731894a6077d1 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 948108074663677f9225fd0574658ca1 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: d5f1c9389ecf52ba839e834780a94549 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_freebayes.yml b/tests/test_freebayes.yml index 6809ac0b4e..d4d85f0a1f 100644 --- a/tests/test_freebayes.yml +++ b/tests/test_freebayes.yml @@ -30,33 +30,19 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: e4ce28ba1c331dc08bc53a0189908f77 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 04d9f20dc5306990eec982a3c5a7d107 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 70b4bbe29bd5e7c4ea39b6caf3316096 - path: results/reports/mosdepth/test/test.md.per-base.bed.gz - md5sum: 2a0c38fb19d6a1f81ca2018e59e7bfcf - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi - md5sum: 0714f8c677277168b9f95d3a43ea5237 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: eb0bc92c253326a109e73af98c9a7d4b - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 9c1d90e0fed14b710098b7724b602aea - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 04d9f20dc5306990eec982a3c5a7d107 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 17dfb78b147488eb8fd450294de4a35e - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: fb6804911f9d437d0251869fe112a528 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 033032cdbb3a2b74dd41dac89628112c - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: eb0bc92c253326a109e73af98c9a7d4b - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -111,25 +97,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -191,61 +167,33 @@ - path: results/reports/markduplicates/test2/test2.md.cram.metrics contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 5a0679057c530e5945c9c5a3a17312dc - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: dcc9ab2bf3248903e02d8da87e678977 - path: results/reports/mosdepth/test/test.md.per-base.bed.gz - md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi - md5sum: b0ab630c3241fbd7581b7a38d944ff8b - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 91e0d531f1bab64711ecefe52bfc8255 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 0b3162def977123809598639f7698121 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: a8455eb2947de529abfa62b303986e0f - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: d9fa560ff78ae106cfee9db2c90801b5 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 4816eeb9af254ca40177b08cf11b98d2 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 91e0d531f1bab64711ecefe52bfc8255 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt - md5sum: f25166c3a0051bb4d8c11a210278de6c - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt - md5sum: 3211135329e4077bd9bf0ba488e14371 - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt - md5sum: ce0eb6d33c6d0dc720fbc6d1811abef8 - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz - md5sum: 55c160e8f3c8c7761524646426611f6b - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz.csi - md5sum: 4205a09ede17cdbdaad45e3553f73105 - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz - md5sum: 1dd426a45f967a9f37dcddcaea29a582 - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt - md5sum: a1ef7e662ce993da4668e804952014ce - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt - md5sum: 3211135329e4077bd9bf0ba488e14371 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt - md5sum: 70ad653c0c98baeeaf5085f1209a7bdb - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz - md5sum: 250a9f15a7d3f102435fa98adccf48a3 - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz.csi - md5sum: 8072f447199c60f24b01eede8b557333 - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz - md5sum: 1dd426a45f967a9f37dcddcaea29a582 - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -328,37 +276,21 @@ - path: results/reports/markduplicates/test2/test2.md.cram.metrics contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 5a0679057c530e5945c9c5a3a17312dc - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 0010c2396a3173c7cf4983abe2eb6a4c - path: results/reports/mosdepth/test/test.md.per-base.bed.gz - md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi - md5sum: b0ab630c3241fbd7581b7a38d944ff8b - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 5a0679057c530e5945c9c5a3a17312dc - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 0010c2396a3173c7cf4983abe2eb6a4c - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: b0ab630c3241fbd7581b7a38d944ff8b - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt - md5sum: f25166c3a0051bb4d8c11a210278de6c - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt - md5sum: d5e4084de2ea2a0a7b60b2d71c804d4b - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz - md5sum: 55c160e8f3c8c7761524646426611f6b - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz.csi - md5sum: 4205a09ede17cdbdaad45e3553f73105 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt - md5sum: f25166c3a0051bb4d8c11a210278de6c - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt - md5sum: d5e4084de2ea2a0a7b60b2d71c804d4b - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz - md5sum: 55c160e8f3c8c7761524646426611f6b - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz.csi - md5sum: 4205a09ede17cdbdaad45e3553f73105 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_gatk4spark.yml b/tests/test_gatk4spark.yml index 270bbdd775..223c5699a4 100644 --- a/tests/test_gatk4spark.yml +++ b/tests/test_gatk4spark.yml @@ -25,23 +25,14 @@ - path: results/reports/markduplicates/test2/test2.md.cram.metrics # text-based file changes md5sums on reruns - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt - md5sum: 85d38a74ce189b9110c57cd94bc26757 - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt - md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81 - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt - md5sum: 04b69ef7f00199dcea7822a79d2c7bd7 - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz - md5sum: 4e6c360aea7f05d801b2ea5685fe154a - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi - md5sum: 5bf5fc178e4faf2462427502c3666004 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt - md5sum: 85d38a74ce189b9110c57cd94bc26757 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt - md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt - md5sum: 04b69ef7f00199dcea7822a79d2c7bd7 - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz - md5sum: 4e6c360aea7f05d801b2ea5685fe154a - path: results/reports/samtools/test2/test2.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test2/test2.recal.cram.stats @@ -78,7 +69,6 @@ - path: results/reports/markduplicates should_exist: false - path: results/reports/mosdepth - should_exist: false - path: results/reports/samtools should_exist: false - name: Run save_output_as_bam with gatk4 spark @@ -109,25 +99,15 @@ - path: results/reports/markduplicates/test2/test2.md.cram.metrics # text-based file changes md5sums on reruns - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt - md5sum: 85d38a74ce189b9110c57cd94bc26757 - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt - md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81 - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt - md5sum: 04b69ef7f00199dcea7822a79d2c7bd7 - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz - md5sum: 4e6c360aea7f05d801b2ea5685fe154a - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi - md5sum: 5bf5fc178e4faf2462427502c3666004 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt - md5sum: 85d38a74ce189b9110c57cd94bc26757 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt - md5sum: 286d57b7d9b3a95ef18ab2eb7f913d81 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt - md5sum: 04b69ef7f00199dcea7822a79d2c7bd7 - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz - md5sum: 4e6c360aea7f05d801b2ea5685fe154a - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi - md5sum: 5bf5fc178e4faf2462427502c3666004 - path: results/reports/samtools/test2/test2.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test2/test2.recal.cram.stats diff --git a/tests/test_haplotypecaller.yml b/tests/test_haplotypecaller.yml index 937198c429..7912e49909 100644 --- a/tests/test_haplotypecaller.yml +++ b/tests/test_haplotypecaller.yml @@ -35,15 +35,10 @@ - path: results/haplotypecaller should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with haplotypecaller without intervals @@ -90,11 +85,7 @@ - path: results/haplotypecaller should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 4f0d231060cbde4efdd673863bd2fb59 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: bc1df47d46f818fee5275975925d769a - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_haplotypecaller_skip_filter.yml b/tests/test_haplotypecaller_skip_filter.yml index 5741547e4f..b96157f868 100644 --- a/tests/test_haplotypecaller_skip_filter.yml +++ b/tests/test_haplotypecaller_skip_filter.yml @@ -39,15 +39,10 @@ - path: results/haplotypecaller should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with haplotypecaller without intervals and skip filter command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --skip_tools haplotypecaller_filter --no_intervals --outdir results @@ -93,11 +88,7 @@ - path: results/haplotypecaller should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 4f0d231060cbde4efdd673863bd2fb59 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: bc1df47d46f818fee5275975925d769a - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_intervals.yml b/tests/test_intervals.yml index df0abfdfa0..21326859d3 100644 --- a/tests/test_intervals.yml +++ b/tests/test_intervals.yml @@ -26,33 +26,19 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: e4ce28ba1c331dc08bc53a0189908f77 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 04d9f20dc5306990eec982a3c5a7d107 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 70b4bbe29bd5e7c4ea39b6caf3316096 - path: results/reports/mosdepth/test/test.md.per-base.bed.gz - md5sum: 2a0c38fb19d6a1f81ca2018e59e7bfcf - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi - md5sum: 0714f8c677277168b9f95d3a43ea5237 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: eb0bc92c253326a109e73af98c9a7d4b - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 9c1d90e0fed14b710098b7724b602aea - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 04d9f20dc5306990eec982a3c5a7d107 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 17dfb78b147488eb8fd450294de4a35e - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: fb6804911f9d437d0251869fe112a528 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 033032cdbb3a2b74dd41dac89628112c - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: eb0bc92c253326a109e73af98c9a7d4b - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -89,21 +75,13 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -142,25 +120,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 0aaee6da65050bedcd40b9fbf0622873 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 544e02fcca548749a0af758d0a2df352 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_joint_germline.yml b/tests/test_joint_germline.yml index 28269bcc66..badaf3c807 100644 --- a/tests/test_joint_germline.yml +++ b/tests/test_joint_germline.yml @@ -31,26 +31,16 @@ - path: results/haplotypecaller should_exist: false - path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testN/testN.recal.cram.stats - path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt - md5sum: ba97ed85645f77da6f3adad138b3cdb4 - path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt - md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b - path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt - md5sum: a937108cbf24c1430b79c861234ce22b - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz - md5sum: d2b579a74bf8d858f82869f073056252 - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testT/testT.recal.cram.stats - name: Run joint germline variant calling with haplotypecaller all intervals at once command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --dbsnp_vqsr false --known_snps_vqsr false --known_indels_vqsr false --nucleotides_per_second 100 --outdir results @@ -85,26 +75,16 @@ - path: results/haplotypecaller should_exist: false - path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testN/testN.recal.cram.stats - path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt - md5sum: ba97ed85645f77da6f3adad138b3cdb4 - path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt - md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b - path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt - md5sum: a937108cbf24c1430b79c861234ce22b - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz - md5sum: d2b579a74bf8d858f82869f073056252 - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testT/testT.recal.cram.stats - name: Run joint germline variant calling with haplotypecaller with Stub for VQSR command: nextflow run main.nf -profile test,tools_germline --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --step variant_calling --joint_germline --outdir results -stub-run @@ -144,24 +124,14 @@ - path: results/haplotypecaller should_exist: false - path: results/reports/mosdepth/testN/testN.recal.global.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testN/testN.recal.region.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testN/testN.recal.summary.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz - md5sum: 1a60c330fb42841e8dcf3cd507a70bfc - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/samtools/testN/testN.recal.cram.stats - path: results/reports/mosdepth/testT/testT.recal.global.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testT/testT.recal.region.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testT/testT.recal.summary.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz - md5sum: 1a60c330fb42841e8dcf3cd507a70bfc - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/samtools/testT/testT.recal.cram.stats diff --git a/tests/test_manta.yml b/tests/test_manta.yml index 2d4fefe378..8b9dfbd168 100644 --- a/tests/test_manta.yml +++ b/tests/test_manta.yml @@ -23,15 +23,10 @@ - path: results/manta should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on germline sample with manta without intervals command: nextflow run main.nf -profile test,tools_germline --tools manta --no_intervals --outdir results @@ -65,13 +60,9 @@ - path: results/manta should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on tumor_only sample with manta command: nextflow run main.nf -profile test,tools_tumoronly --tools manta --outdir results @@ -98,15 +89,10 @@ - path: results/manta should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on tumor_only sample with manta without intervals command: nextflow run main.nf -profile test,tools_tumoronly --tools manta --no_intervals --outdir results @@ -140,13 +126,9 @@ - path: results/manta should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on somatic sample with manta command: nextflow run main.nf -profile test,tools_somatic --tools manta --outdir results @@ -197,27 +179,17 @@ - path: results/manta should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with manta without intervals @@ -276,22 +248,14 @@ - path: results/manta should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test diff --git a/tests/test_markduplicates_from_bam.yml b/tests/test_markduplicates_from_bam.yml index 1619bc2545..ab436a7ce2 100644 --- a/tests/test_markduplicates_from_bam.yml +++ b/tests/test_markduplicates_from_bam.yml @@ -25,25 +25,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986 1178 1178", "100.0 1.911145 0 0"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -71,25 +61,15 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats diff --git a/tests/test_markduplicates_from_cram.yml b/tests/test_markduplicates_from_cram.yml index e70d9e2325..ff28636112 100644 --- a/tests/test_markduplicates_from_cram.yml +++ b/tests/test_markduplicates_from_cram.yml @@ -25,25 +25,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986 1178 1178", "100.0 1.911145 0 0"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -68,25 +58,15 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: f1f1ad86fc280bced1888a5d7d25a3f2 - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: 2beb1a78ededc5d8be591e5449849087 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: c5d0be930ffc9e562f21519a0d488d5d - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats diff --git a/tests/test_mpileup.yml b/tests/test_mpileup.yml index 25fefd0eb0..c6603211b3 100644 --- a/tests/test_mpileup.yml +++ b/tests/test_mpileup.yml @@ -14,15 +14,10 @@ - path: results/mpileup should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on tumor_only sample to test mpileup without intervals command: nextflow run main.nf -profile test,tools_tumoronly --tools mpileup --no_intervals --outdir results @@ -47,13 +42,9 @@ - path: results/mpileup should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on germline sample to test mpileup command: nextflow run main.nf -profile test,tools_germline --tools mpileup --outdir results @@ -71,15 +62,10 @@ - path: results/mpileup should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on germline sample to test mpileup without intervals command: nextflow run main.nf -profile test,tools_germline --tools mpileup --no_intervals --outdir results @@ -104,11 +90,7 @@ - path: results/mpileup should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample1/sample1.recal.cram.stats diff --git a/tests/test_msisensorpro.yml b/tests/test_msisensorpro.yml index 8a462e305b..5133de900b 100644 --- a/tests/test_msisensorpro.yml +++ b/tests/test_msisensorpro.yml @@ -13,27 +13,17 @@ - path: results/msisensorpro should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Build only index with msisensorpro diff --git a/tests/test_mutect2.yml b/tests/test_mutect2.yml index 28d9f5f933..c5ea0e8b8d 100644 --- a/tests/test_mutect2.yml +++ b/tests/test_mutect2.yml @@ -39,15 +39,10 @@ - path: results/mutect2 should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on tumor only sample with mutect2 without intervals command: nextflow run main.nf -profile test,tools_tumoronly --tools mutect2 --no_intervals --outdir results @@ -97,11 +92,7 @@ - path: results/mutect2 should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample2/sample2.recal.cram.stats diff --git a/tests/test_prepare_recalibration_from_bam.yml b/tests/test_prepare_recalibration_from_bam.yml index b5ab788e78..7095fe98a0 100644 --- a/tests/test_prepare_recalibration_from_bam.yml +++ b/tests/test_prepare_recalibration_from_bam.yml @@ -21,15 +21,10 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/preprocessing/mapped/ @@ -75,7 +70,6 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth - should_exist: false - path: results/reports/samtools_stats should_exist: false - path: results/preprocessing/mapped/ diff --git a/tests/test_prepare_recalibration_from_cram.yml b/tests/test_prepare_recalibration_from_cram.yml index d207c6f190..c002b299c3 100644 --- a/tests/test_prepare_recalibration_from_cram.yml +++ b/tests/test_prepare_recalibration_from_cram.yml @@ -15,15 +15,10 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/preprocessing/mapped/ @@ -69,13 +64,9 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - should_exist: false - path: results/reports/samtools/test/test.recal.cram.stats should_exist: false - path: results/preprocessing/mapped/ diff --git a/tests/test_recalibrate_from_bam.yml b/tests/test_recalibrate_from_bam.yml index 41d0c91e4a..4edc5161dd 100644 --- a/tests/test_recalibrate_from_bam.yml +++ b/tests/test_recalibrate_from_bam.yml @@ -17,15 +17,10 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/preprocessing/mapped/ @@ -72,13 +67,9 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - should_exist: false - path: results/reports/samtools/test/test.recal.cram.stats should_exist: false - path: results/preprocessing/mapped/ diff --git a/tests/test_recalibrate_from_cram.yml b/tests/test_recalibrate_from_cram.yml index 5f5d0badd3..779fbb148f 100644 --- a/tests/test_recalibrate_from_cram.yml +++ b/tests/test_recalibrate_from_cram.yml @@ -13,15 +13,10 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/preprocessing/mapped/ @@ -68,13 +63,9 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - should_exist: false - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - should_exist: false - path: results/reports/samtools/test/test.recal.cram.stats should_exist: false - path: results/preprocessing/mapped/ diff --git a/tests/test_save_mapped.yml b/tests/test_save_mapped.yml index f7f7005724..251e7ddacc 100644 --- a/tests/test_save_mapped.yml +++ b/tests/test_save_mapped.yml @@ -34,25 +34,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_save_output_as_bam_only.yml b/tests/test_save_output_as_bam_only.yml index ffcf66e331..6e47260424 100644 --- a/tests/test_save_output_as_bam_only.yml +++ b/tests/test_save_output_as_bam_only.yml @@ -28,25 +28,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 839108358878ada89e1eaddf6e0541ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d394814b86ab2bf1bc8733546a12517a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5f9c60279af78e3aeafc96a8c11fb35f - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_sentieon_aligner_bwamem.yml b/tests/test_sentieon_aligner_bwamem.yml index 6bf048cecb..36f5e66683 100644 --- a/tests/test_sentieon_aligner_bwamem.yml +++ b/tests/test_sentieon_aligner_bwamem.yml @@ -50,25 +50,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 9afbcd5e44b62b3947e47af850a66188 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 3bd6a6f7127394802d9a7c7d559072ee - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 72ae14370dfdaab906e50d0552c90119 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 9afbcd5e44b62b3947e47af850a66188 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 3bd6a6f7127394802d9a7c7d559072ee - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 72ae14370dfdaab906e50d0552c90119 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -136,25 +126,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 9afbcd5e44b62b3947e47af850a66188 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 3bd6a6f7127394802d9a7c7d559072ee - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 72ae14370dfdaab906e50d0552c90119 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 9afbcd5e44b62b3947e47af850a66188 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 3bd6a6f7127394802d9a7c7d559072ee - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 72ae14370dfdaab906e50d0552c90119 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats @@ -190,25 +170,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 17094 1534 168 1046782 12429 197 0 0.635998", "1.0 0.999991 1171"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 9afbcd5e44b62b3947e47af850a66188 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 3bd6a6f7127394802d9a7c7d559072ee - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 72ae14370dfdaab906e50d0552c90119 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: b61e1acee11a6ddf7ce3232a5948a6a0 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1a382f98d488d2ae3df83a0d87caafc1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 9afbcd5e44b62b3947e47af850a66188 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 3bd6a6f7127394802d9a7c7d559072ee - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 72ae14370dfdaab906e50d0552c90119 - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_sentieon_dedup_from_bam.yml b/tests/test_sentieon_dedup_from_bam.yml index 306ae5634f..48d55177e0 100644 --- a/tests/test_sentieon_dedup_from_bam.yml +++ b/tests/test_sentieon_dedup_from_bam.yml @@ -27,25 +27,15 @@ - path: results/reports/sentieon_dedup/test/test.dedup.cram.metrics contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986", "100.0 1.911145"] - path: results/reports/mosdepth/test/test.dedup.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.dedup.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.dedup.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.dedup.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.dedup.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/samtools/test/test.dedup.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_sentieon_dedup_from_cram.yml b/tests/test_sentieon_dedup_from_cram.yml index abf6f57da6..9f826c502c 100644 --- a/tests/test_sentieon_dedup_from_cram.yml +++ b/tests/test_sentieon_dedup_from_cram.yml @@ -27,25 +27,15 @@ - path: results/reports/sentieon_dedup/test/test.dedup.cram.metrics contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986", "2.0 1.476740", "3.0 1.704038"] - path: results/reports/mosdepth/test/test.dedup.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.dedup.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.dedup.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.dedup.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.dedup.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - # binary changes md5sums on reruns - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - # binary changes md5sums on reruns - path: results/reports/samtools/test/test.dedup.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_sentieon_dnascope.yml b/tests/test_sentieon_dnascope.yml index 889954b90e..142cd73156 100644 --- a/tests/test_sentieon_dnascope.yml +++ b/tests/test_sentieon_dnascope.yml @@ -34,15 +34,10 @@ - path: results/dnascope should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons dnascope without intervals command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --no_intervals --outdir results @@ -87,13 +82,9 @@ - path: results/sentieon_dnascope should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 4f0d231060cbde4efdd673863bd2fb59 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: bc1df47d46f818fee5275975925d769a - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons dnascope output gvcf @@ -135,15 +126,10 @@ - path: results/dnascope should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons dnascope output both gvcf and vcf command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --outdir results --sentieon_dnascope_emit_mode variant,gvcf @@ -176,13 +162,8 @@ - path: results/dnascope should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_sentieon_dnascope_skip_filter.yml b/tests/test_sentieon_dnascope_skip_filter.yml index 7c37449a26..b3740ca749 100644 --- a/tests/test_sentieon_dnascope_skip_filter.yml +++ b/tests/test_sentieon_dnascope_skip_filter.yml @@ -32,15 +32,10 @@ - path: results/sentieon_dnascope should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieon dnascope without intervals and skip filter command: nextflow run main.nf -profile test,targeted,software_license --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_dnascope --step variant_calling --skip_tools dnascope_filter --no_intervals --outdir results @@ -83,11 +78,7 @@ - path: results/sentieon_dnascope should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 4f0d231060cbde4efdd673863bd2fb59 - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: bc1df47d46f818fee5275975925d769a - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_sentieon_haplotyper.yml b/tests/test_sentieon_haplotyper.yml index 948e7a37bd..201d07a5be 100644 --- a/tests/test_sentieon_haplotyper.yml +++ b/tests/test_sentieon_haplotyper.yml @@ -34,14 +34,10 @@ - path: results/haplotyper should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons haplotyper without intervals command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --no_intervals --outdir results @@ -86,12 +82,9 @@ - path: results/sentieon_haplotyper should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: bc1df47d46f818fee5275975925d769a - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons haplotyper output gvcf command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode gvcf @@ -132,14 +125,10 @@ - path: results/haplotyper should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons haplotyper output both gvcf and vcf command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --outdir results --sentieon_haplotyper_emit_mode variant,gvcf @@ -172,14 +161,10 @@ - path: results/haplotyper should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieons haplotyper and gatk haplotypecaller command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller,sentieon_haplotyper --step variant_calling --outdir results @@ -225,12 +210,8 @@ - path: results/haplotyper should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_sentieon_haplotyper_joint_germline.yml b/tests/test_sentieon_haplotyper_joint_germline.yml index 1e4d5d82db..7dfa2d5d1d 100644 --- a/tests/test_sentieon_haplotyper_joint_germline.yml +++ b/tests/test_sentieon_haplotyper_joint_germline.yml @@ -27,26 +27,16 @@ - path: results/haplotyper should_exist: false - path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testN/testN.recal.cram.stats - path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt - md5sum: ba97ed85645f77da6f3adad138b3cdb4 - path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt - md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b - path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt - md5sum: a937108cbf24c1430b79c861234ce22b - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz - md5sum: d2b579a74bf8d858f82869f073056252 - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testT/testT.recal.cram.stats - name: Run joint germline variant calling with sentieon haplotyper all intervals at once command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf --nucleotides_per_second 100 @@ -75,26 +65,16 @@ - path: results/haplotyper should_exist: false - path: results/reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt - md5sum: 3a2030e5e8af7bc12720c3a5592bf921 - path: results/reports/mosdepth/testN/testN.recal.mosdepth.summary.txt - md5sum: 615c5c5019d88045a9ff5bbe6e63d270 - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz - md5sum: 9f1ea20e7461db948ba21f70c4d1b3ba - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testN/testN.recal.cram.stats - path: results/reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt - md5sum: ba97ed85645f77da6f3adad138b3cdb4 - path: results/reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt - md5sum: a7eb835371dd0aaf347ccca7ebe1eb3b - path: results/reports/mosdepth/testT/testT.recal.mosdepth.summary.txt - md5sum: a937108cbf24c1430b79c861234ce22b - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz - md5sum: d2b579a74bf8d858f82869f073056252 - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi - md5sum: 5c00a1d457c387d6e71848a6d897e309 - path: results/reports/samtools/testT/testT.recal.cram.stats - name: Run joint germline variant calling with sentieon haplotyper with stub for VQSR command: nextflow run main.nf -profile test,software_license,tools_germline --sentieon_extension --input ./tests/csv/3.0/mapped_joint_bam.csv --tools sentieon_haplotyper --step variant_calling --joint_germline --outdir results --sentieon_haplotyper_emit_mode gvcf -stub-run @@ -123,24 +103,14 @@ - path: results/haplotyper should_exist: false - path: results/reports/mosdepth/testN/testN.recal.global.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testN/testN.recal.region.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testN/testN.recal.summary.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz - md5sum: 1a60c330fb42841e8dcf3cd507a70bfc - path: results/reports/mosdepth/testN/testN.recal.regions.bed.gz.csi - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/samtools/testN/testN.recal.cram.stats - path: results/reports/mosdepth/testT/testT.recal.global.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testT/testT.recal.region.dist.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testT/testT.recal.summary.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz - md5sum: 1a60c330fb42841e8dcf3cd507a70bfc - path: results/reports/mosdepth/testT/testT.recal.regions.bed.gz.csi - md5sum: d41d8cd98f00b204e9800998ecf8427e - path: results/reports/samtools/testT/testT.recal.cram.stats diff --git a/tests/test_sentieon_haplotyper_skip_filter.yml b/tests/test_sentieon_haplotyper_skip_filter.yml index 2f8beaba75..7328e9a4ec 100644 --- a/tests/test_sentieon_haplotyper_skip_filter.yml +++ b/tests/test_sentieon_haplotyper_skip_filter.yml @@ -34,12 +34,9 @@ - path: results/sentieon_haplotyper should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: bc1df47d46f818fee5275975925d769a - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats - name: Run variant calling on germline sample with sentieon haplotyper without intervals and skip filter command: nextflow run main.nf -profile test,software_license,targeted --sentieon_extension --input ./tests/csv/3.0/mapped_single_bam.csv --tools sentieon_haplotyper --step variant_calling --skip_tools haplotyper_filter --no_intervals --outdir results @@ -84,10 +81,7 @@ - path: results/sentieon_haplotyper should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: e82e90c7d508a135b5a8a7cd6933452e - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: bc1df47d46f818fee5275975925d769a - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml index cde62c04d2..93718954c8 100644 --- a/tests/test_skip_markduplicates.yml +++ b/tests/test_skip_markduplicates.yml @@ -22,25 +22,15 @@ # binary changes md5sums on reruns - path: results/reports/fastqc/test-test_L1 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1653d9aa161a78d8574269083f7d92f1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 1653d9aa161a78d8574269083f7d92f1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats @@ -78,25 +68,15 @@ # binary changes md5sums on reruns - path: results/reports/fastqc/test-test_L1 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1653d9aa161a78d8574269083f7d92f1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 1653d9aa161a78d8574269083f7d92f1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats @@ -132,25 +112,15 @@ # binary changes md5sums on reruns - path: results/reports/fastqc/test-test_L1 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 1653d9aa161a78d8574269083f7d92f1 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: 3ab32cc98996e0f12b8088b99dd1e2d1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 1653d9aa161a78d8574269083f7d92f1 - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: b8874be5d830a2d03d42bccad7c996d3 - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: a5b158106aee6827a758aaf9b4f0f03a - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: 3fbfb2754f4f27fa8238e0e231f1f360 - path: results/reports/samtools/test/test.recal.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.sorted.cram.stats diff --git a/tests/test_strelka.yml b/tests/test_strelka.yml index e222a00fa5..b2b25672a2 100644 --- a/tests/test_strelka.yml +++ b/tests/test_strelka.yml @@ -77,49 +77,29 @@ - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on germline sample with strelka @@ -151,15 +131,10 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on germline sample with strelka without intervals command: nextflow run main.nf -profile test,tools_germline --tools strelka --no_intervals --outdir results @@ -197,13 +172,9 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on tumor only sample with strelka command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka --outdir results @@ -234,15 +205,10 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on tumor only sample with strelka without intervals command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka --no_intervals --outdir results @@ -280,13 +246,9 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample2/sample2.recal.cram.stats - name: Run variant calling on somatic sample with strelka command: nextflow run main.nf -profile test,tools_somatic --tools strelka --outdir results @@ -341,27 +303,17 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with strelka without intervals @@ -424,22 +376,14 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test diff --git a/tests/test_strelka_bp.yml b/tests/test_strelka_bp.yml index d2ec3549e3..f5954de37c 100644 --- a/tests/test_strelka_bp.yml +++ b/tests/test_strelka_bp.yml @@ -89,27 +89,17 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with Strelka BP without intervals @@ -210,22 +200,14 @@ - path: results/strelka should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test diff --git a/tests/test_tiddit.yml b/tests/test_tiddit.yml index 8d0c5b718c..7d397e08a4 100644 --- a/tests/test_tiddit.yml +++ b/tests/test_tiddit.yml @@ -45,27 +45,17 @@ - path: results/tiddit should_exist: false - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on germline sample with tiddit @@ -95,15 +85,10 @@ - path: results/tiddit should_exist: false - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats - name: Run variant calling on tumor_only sample with tiddit command: nextflow run main.nf -profile test,tools_tumoronly --tools tiddit --outdir results @@ -132,13 +117,8 @@ - path: results/tiddit should_exist: false - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats diff --git a/tests/test_tools_manually.yml b/tests/test_tools_manually.yml index 23b005ac7a..fe1642b3c3 100644 --- a/tests/test_tools_manually.yml +++ b/tests/test_tools_manually.yml @@ -35,27 +35,17 @@ - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_normalLogR.txt md5sum: 05418a7d814db11808172a4f57d040a1 - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with mutect2 without intervals @@ -107,23 +97,15 @@ - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.tbi # binary changes md5sums on reruns - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: d2775eb102acc5950f7f53883dcb503d - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz - md5sum: 54431f155c9538809e8caf99d1a75ec7 - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi - md5sum: c67dcd711b096eb42f43784d5eadbc0d - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 0a7300e56eda6fba7c7564f00aa000f0 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz - md5sum: 3de4a9f4da2f2b4909ef192452a8d211 - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi - md5sum: cfb07b0ba46e8468b4342edb243536f3 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run variant calling on somatic sample with mutect2 @@ -168,27 +150,17 @@ - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.tbi # binary changes md5sums on reruns - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample4/sample4.recal.cram.stats # conda changes md5sums for test - name: Run joint calling on tumor only samples with mutect2 @@ -239,15 +211,10 @@ - path: results/variant_calling/mutect2/test/test.mutect2.vcf.gz.tbi # binary changes md5sums on reruns - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - name: Run joint calling on somatic samples with mutect2 @@ -299,39 +266,24 @@ - path: results/variant_calling/mutect2/test/test.mutect2.vcf.gz.tbi # binary changes md5sums on reruns - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - md5sum: 69e29702ef01fd8f6c7a5468fc35a16a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - md5sum: 6ec49cd7d510c2eb3d9d90fdb79b783a - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - md5sum: 103098d0bf76ed82d2b87d5f242b099a - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - md5sum: b5888cf7395c57d39879a5faa6159eb3 - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - md5sum: 9cb0ad7039a3b703d16ca7d5b835c0ee - path: results/reports/samtools/sample1/sample1.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample2/sample2.recal.cram.stats # conda changes md5sums for test - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - md5sum: f2dcd00a64947c49e8e4b93c2f4fbf27 - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - md5sum: 39005ffaac22871ffaaf19656fe69c5b - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - md5sum: 68d4b98f17361fddf73052ead34fa370 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - md5sum: 2819e995eafded35f53328c4ec19ba58 - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - md5sum: 393c2749068304d8545b501b9d4658e4 - path: results/reports/samtools/sample3/sample3.recal.cram.stats # conda changes md5sums for test - name: Run full pipeline on tumoronly with most tools diff --git a/tests/test_tumor_normal_pair.yml b/tests/test_tumor_normal_pair.yml index 3bb6404249..711e494ca1 100644 --- a/tests/test_tumor_normal_pair.yml +++ b/tests/test_tumor_normal_pair.yml @@ -39,45 +39,25 @@ - path: results/reports/markduplicates/test2/test2.md.cram.metrics contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 76fa71922a3f748e507c2364c531dfcb - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: abc5df85e302b79985627888870882da - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: d536456436eb275159b8c6af83213d80 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 16cda2fae13c766a7f241600966343f4 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 05d571f8d51ca6b1bde804d7a6d999af - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 76fa71922a3f748e507c2364c531dfcb - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: abc5df85e302b79985627888870882da - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: d536456436eb275159b8c6af83213d80 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 16cda2fae13c766a7f241600966343f4 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 05d571f8d51ca6b1bde804d7a6d999af - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt - md5sum: 2020cf6dfc7ddca020c921dd9f0549b7 - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt - md5sum: 38ff8b38c33b9231f047fea8ea830aae - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt - md5sum: 8b991358768cade225470a07cd34f573 - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz - md5sum: 880c996fce059c19c4551b11b3c6f58e - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi - md5sum: eba5aca0b8f72759192bbdd29330278e - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt - md5sum: 2020cf6dfc7ddca020c921dd9f0549b7 - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt - md5sum: 38ff8b38c33b9231f047fea8ea830aae - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt - md5sum: 8b991358768cade225470a07cd34f573 - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz - md5sum: 880c996fce059c19c4551b11b3c6f58e - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi - md5sum: eba5aca0b8f72759192bbdd29330278e - path: results/reports/samtools/test/test.md.cram.stats # conda changes md5sums for test - path: results/reports/samtools/test/test.recal.cram.stats diff --git a/tests/test_umi.yml b/tests/test_umi.yml index 69d8cf2433..0c8392f40e 100644 --- a/tests/test_umi.yml +++ b/tests/test_umi.yml @@ -27,25 +27,15 @@ - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 0 2804 3 4 0 77 0 0.027461 50115", "1.0 1 2651 2651", "12.0 8.9868 0 0"] - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 09d22913aa50a0207f97a3f85b182c6e - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 9359ba1c4e09aa47cc95c9134f526675 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 9bbea5e4d213a51f501c2aadff8d4526 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: ef4426cd1d433464004bb39d483abad9 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: d0713716f63ac573f4a3385733e9a537 - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 09d22913aa50a0207f97a3f85b182c6e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 9359ba1c4e09aa47cc95c9134f526675 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 9bbea5e4d213a51f501c2aadff8d4526 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: ef4426cd1d433464004bb39d483abad9 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: d0713716f63ac573f4a3385733e9a537 - path: results/reports/samtools/test/test.md.cram.stats # text-based file changes md5sums on reruns - path: results/reports/samtools/test/test.recal.cram.stats From 5f2dc64f5c7bbf37cb841ddc9bea983daff730c1 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Sat, 4 May 2024 12:59:42 +0200 Subject: [PATCH 2/2] Apply suggestions from code review --- tests/test_gatk4spark.yml | 1 + tests/test_prepare_recalibration_from_bam.yml | 1 + tests/test_prepare_recalibration_from_cram.yml | 4 ++++ tests/test_recalibrate_from_bam.yml | 4 ++++ tests/test_recalibrate_from_cram.yml | 4 ++++ 5 files changed, 14 insertions(+) diff --git a/tests/test_gatk4spark.yml b/tests/test_gatk4spark.yml index 223c5699a4..cdb2cf3292 100644 --- a/tests/test_gatk4spark.yml +++ b/tests/test_gatk4spark.yml @@ -69,6 +69,7 @@ - path: results/reports/markduplicates should_exist: false - path: results/reports/mosdepth + should_exist: false - path: results/reports/samtools should_exist: false - name: Run save_output_as_bam with gatk4 spark diff --git a/tests/test_prepare_recalibration_from_bam.yml b/tests/test_prepare_recalibration_from_bam.yml index 7095fe98a0..335a67deed 100644 --- a/tests/test_prepare_recalibration_from_bam.yml +++ b/tests/test_prepare_recalibration_from_bam.yml @@ -70,6 +70,7 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth + should_exist: false - path: results/reports/samtools_stats should_exist: false - path: results/preprocessing/mapped/ diff --git a/tests/test_prepare_recalibration_from_cram.yml b/tests/test_prepare_recalibration_from_cram.yml index c002b299c3..6e362ccd7b 100644 --- a/tests/test_prepare_recalibration_from_cram.yml +++ b/tests/test_prepare_recalibration_from_cram.yml @@ -64,9 +64,13 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + should_exist: false - path: results/reports/samtools/test/test.recal.cram.stats should_exist: false - path: results/preprocessing/mapped/ diff --git a/tests/test_recalibrate_from_bam.yml b/tests/test_recalibrate_from_bam.yml index 4edc5161dd..fb96a3d305 100644 --- a/tests/test_recalibrate_from_bam.yml +++ b/tests/test_recalibrate_from_bam.yml @@ -67,9 +67,13 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + should_exist: false - path: results/reports/samtools/test/test.recal.cram.stats should_exist: false - path: results/preprocessing/mapped/ diff --git a/tests/test_recalibrate_from_cram.yml b/tests/test_recalibrate_from_cram.yml index 779fbb148f..9e53da4f2d 100644 --- a/tests/test_recalibrate_from_cram.yml +++ b/tests/test_recalibrate_from_cram.yml @@ -63,9 +63,13 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + should_exist: false - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + should_exist: false - path: results/reports/samtools/test/test.recal.cram.stats should_exist: false - path: results/preprocessing/mapped/