From 31be1151a981b5431a1c00fcf594d962bc753eed Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 3 Mar 2025 15:38:24 +0100 Subject: [PATCH 01/14] add tests for normalization and concat + normaliz --- tests/config/pytesttags.yml | 34 -- ...test => postprocess_concatenation.nf.test} | 0 ...=> postprocess_concatenation.nf.test.snap} | 0 ...rocess_concatenation_normalization.nf.test | 47 +++ ...s_concatenation_normalization.nf.test.snap | 265 +++++++++++++ tests/postprocess_normalization.nf.test | 46 +++ tests/postprocess_normalization.nf.test.snap | 375 ++++++++++++++++++ 7 files changed, 733 insertions(+), 34 deletions(-) rename tests/{concatenation.nf.test => postprocess_concatenation.nf.test} (100%) rename tests/{concatenation.nf.test.snap => postprocess_concatenation.nf.test.snap} (100%) create mode 100644 tests/postprocess_concatenation_normalization.nf.test create mode 100644 tests/postprocess_concatenation_normalization.nf.test.snap create mode 100644 tests/postprocess_normalization.nf.test create mode 100644 tests/postprocess_normalization.nf.test.snap diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml index b3c820f60a..b72fbb0fa4 100644 --- a/tests/config/pytesttags.yml +++ b/tests/config/pytesttags.yml @@ -341,40 +341,6 @@ tiddit: - tests/csv/3.0/recalibrated_tumoronly.csv - tests/test_tiddit.yml -# postprocessing - -## normalize all vcfs -normalize_vcfs: - - conf/modules/post_variant_calling.config - - modules/nf-core/bcftools/concat/** - - modules/nf-core/bcftools/mpileup/** - - modules/nf-core/bcftools/norm/** - - modules/nf-core/bcftools/sort/** - - modules/nf-core/deepvariant/** - - modules/nf-core/freebayes/** - - modules/nf-core/gatk4/haplotypecaller/** - - modules/nf-core/gatk4/mergevcfs/** - - modules/nf-core/manta/germline/** - - modules/nf-core/samtools/mpileup/** - - modules/nf-core/strelka/germline/** - - modules/nf-core/tabix/bgziptabix/** - - modules/nf-core/tabix/tabix/** - - modules/nf-core/tiddit/sv/** - - subworkflows/local/bam_variant_calling_deepvariant/** - - subworkflows/local/bam_variant_calling_freebayes/** - - subworkflows/local/bam_variant_calling_germline_all/** - - subworkflows/local/bam_variant_calling_germline_manta/** - - subworkflows/local/bam_variant_calling_haplotypecaller/** - - subworkflows/local/bam_variant_calling_mpileup/** - - subworkflows/local/bam_variant_calling_single_strelka/** - - subworkflows/local/bam_variant_calling_single_tiddit/** - - subworkflows/local/bam_variant_calling_somatic_all/** - - subworkflows/local/bam_variant_calling_tumor_only_all/** - - subworkflows/local/post_variantcalling/** - - subworkflows/local/vcf_normalization/** - - tests/csv/3.0/mapped_joint_bam.csv - - tests/test_normalize_vcfs.yml - # sampleqc ## ngscheckmate diff --git a/tests/concatenation.nf.test b/tests/postprocess_concatenation.nf.test similarity index 100% rename from tests/concatenation.nf.test rename to tests/postprocess_concatenation.nf.test diff --git a/tests/concatenation.nf.test.snap b/tests/postprocess_concatenation.nf.test.snap similarity index 100% rename from tests/concatenation.nf.test.snap rename to tests/postprocess_concatenation.nf.test.snap diff --git a/tests/postprocess_concatenation_normalization.nf.test b/tests/postprocess_concatenation_normalization.nf.test new file mode 100644 index 0000000000..20f374e84d --- /dev/null +++ b/tests/postprocess_concatenation_normalization.nf.test @@ -0,0 +1,47 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + tag "pipeline_sarek" + + test("-profile test --normalize_vcfs --concatenate_vcfs --tools freebayes,haplotypecaller") { + + when { + params { + + input = "${projectDir}/tests/csv/3.0/mapped_joint_bam.csv" + step = 'variant_calling' + normalize_vcfs = true + concatenate_vcfs = true + tools = 'freebayes,haplotypecaller' + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // vcf_files: All vcf files + def vcf_files = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path, + // All vcf files + vcf_files.collect { file -> [file.getName(), path(file.toString()).vcf.variantsMD5] } + ).match() } + ) + } + } +} diff --git a/tests/postprocess_concatenation_normalization.nf.test.snap b/tests/postprocess_concatenation_normalization.nf.test.snap new file mode 100644 index 0000000000..c78d8d1539 --- /dev/null +++ b/tests/postprocess_concatenation_normalization.nf.test.snap @@ -0,0 +1,265 @@ +{ + "-profile test --concatenate_vcfs --tools freebayes,haplotypecaller": { + "content": [ + 51, + { + "ADD_INFO_TO_VCF": { + "gawk": "5.1.0" + }, + "BCFTOOLS_SORT": { + "bcftools": 1.2 + }, + "BCFTOOLS_STATS": { + "bcftools": 1.2 + }, + "CNNSCOREVARIANTS": { + "gatk4": "4.5.0.0" + }, + "FILTERVARIANTTRANCHES": { + "gatk4": "4.5.0.0" + }, + "FREEBAYES": { + "freebayes": "1.3.6" + }, + "GATK4_HAPLOTYPECALLER": { + "gatk4": "4.5.0.0" + }, + "GERMLINE_VCFS_CONCAT": { + "bcftools": 1.2 + }, + "TABIX_EXT_VCF": { + "tabix": 1.2 + }, + "TABIX_GERMLINE_VCFS_CONCAT_SORT": { + "tabix": 1.2 + }, + "TABIX_VC_FREEBAYES": { + "tabix": 1.2 + }, + "VCFTOOLS_TSTV_COUNT": { + "vcftools": "0.1.16" + }, + "Workflow": { + "nf-core/sarek": "v3.6.0dev" + } + }, + [ + "csv", + "csv/variantcalled.csv", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/bcftools-stats-subtypes.txt", + "multiqc/multiqc_data/bcftools_stats_indel-lengths.txt", + "multiqc/multiqc_data/bcftools_stats_variant_depths.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc_bcftools_stats.txt", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_data/vcftools_tstv_by_count.txt", + "multiqc/multiqc_data/vcftools_tstv_by_qual.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_variant_depths.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf", + "multiqc/multiqc_plots/pdf/general_stats_table.pdf", + "multiqc/multiqc_plots/pdf/vcftools_tstv_by_count.pdf", + "multiqc/multiqc_plots/pdf/vcftools_tstv_by_qual.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/bcftools-stats-subtypes-cnt.png", + "multiqc/multiqc_plots/png/bcftools-stats-subtypes-pct.png", + "multiqc/multiqc_plots/png/bcftools_stats_indel-lengths.png", + "multiqc/multiqc_plots/png/bcftools_stats_variant_depths.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png", + "multiqc/multiqc_plots/png/general_stats_table.png", + "multiqc/multiqc_plots/png/vcftools_tstv_by_count.png", + "multiqc/multiqc_plots/png/vcftools_tstv_by_qual.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-cnt.svg", + "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-pct.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_variant_depths.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg", + "multiqc/multiqc_plots/svg/general_stats_table.svg", + "multiqc/multiqc_plots/svg/vcftools_tstv_by_count.svg", + "multiqc/multiqc_plots/svg/vcftools_tstv_by_qual.svg", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_sarek_software_mqc_versions.yml", + "reference", + "reports", + "reports/bcftools", + "reports/bcftools/freebayes", + "reports/bcftools/freebayes/testN", + "reports/bcftools/freebayes/testN/testN.freebayes.bcftools_stats.txt", + "reports/bcftools/freebayes/testT", + "reports/bcftools/freebayes/testT/testT.freebayes.bcftools_stats.txt", + "reports/bcftools/haplotypecaller", + "reports/bcftools/haplotypecaller/testN", + "reports/bcftools/haplotypecaller/testN/testN.haplotypecaller.filtered.bcftools_stats.txt", + "reports/bcftools/haplotypecaller/testT", + "reports/bcftools/haplotypecaller/testT/testT.haplotypecaller.filtered.bcftools_stats.txt", + "reports/mosdepth", + "reports/mosdepth/testN", + "reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt", + "reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt", + "reports/mosdepth/testN/testN.recal.mosdepth.summary.txt", + "reports/mosdepth/testN/testN.recal.regions.bed.gz", + "reports/mosdepth/testN/testN.recal.regions.bed.gz.csi", + "reports/mosdepth/testT", + "reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt", + "reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt", + "reports/mosdepth/testT/testT.recal.mosdepth.summary.txt", + "reports/mosdepth/testT/testT.recal.regions.bed.gz", + "reports/mosdepth/testT/testT.recal.regions.bed.gz.csi", + "reports/samtools", + "reports/samtools/testN", + "reports/samtools/testN/testN.recal.cram.stats", + "reports/samtools/testT", + "reports/samtools/testT/testT.recal.cram.stats", + "reports/vcftools", + "reports/vcftools/freebayes", + "reports/vcftools/freebayes/testN", + "reports/vcftools/freebayes/testN/testN.freebayes.FILTER.summary", + "reports/vcftools/freebayes/testN/testN.freebayes.TsTv.count", + "reports/vcftools/freebayes/testN/testN.freebayes.TsTv.qual", + "reports/vcftools/freebayes/testT", + "reports/vcftools/freebayes/testT/testT.freebayes.FILTER.summary", + "reports/vcftools/freebayes/testT/testT.freebayes.TsTv.count", + "reports/vcftools/freebayes/testT/testT.freebayes.TsTv.qual", + "reports/vcftools/haplotypecaller", + "reports/vcftools/haplotypecaller/testN", + "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.filtered.FILTER.summary", + "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.filtered.TsTv.count", + "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.filtered.TsTv.qual", + "reports/vcftools/haplotypecaller/testT", + "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.filtered.FILTER.summary", + "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.filtered.TsTv.count", + "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.filtered.TsTv.qual", + "variant_calling", + "variant_calling/concat", + "variant_calling/concat/testN", + "variant_calling/concat/testN/testN.germline.vcf.gz", + "variant_calling/concat/testN/testN.germline.vcf.gz.tbi", + "variant_calling/concat/testN/versions.yml", + "variant_calling/concat/testT", + "variant_calling/concat/testT/testT.germline.vcf.gz", + "variant_calling/concat/testT/testT.germline.vcf.gz.tbi", + "variant_calling/concat/testT/versions.yml", + "variant_calling/freebayes", + "variant_calling/freebayes/testN", + "variant_calling/freebayes/testN/testN.freebayes.vcf.gz", + "variant_calling/freebayes/testN/testN.freebayes.vcf.gz.tbi", + "variant_calling/freebayes/testT", + "variant_calling/freebayes/testT/testT.freebayes.vcf.gz", + "variant_calling/freebayes/testT/testT.freebayes.vcf.gz.tbi", + "variant_calling/haplotypecaller", + "variant_calling/haplotypecaller/testN", + "variant_calling/haplotypecaller/testN/testN.haplotypecaller.filtered.vcf.gz", + "variant_calling/haplotypecaller/testN/testN.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/haplotypecaller/testN/testN.haplotypecaller.vcf.gz", + "variant_calling/haplotypecaller/testN/testN.haplotypecaller.vcf.gz.tbi", + "variant_calling/haplotypecaller/testT", + "variant_calling/haplotypecaller/testT/testT.haplotypecaller.filtered.vcf.gz", + "variant_calling/haplotypecaller/testT/testT.haplotypecaller.filtered.vcf.gz.tbi", + "variant_calling/haplotypecaller/testT/testT.haplotypecaller.vcf.gz", + "variant_calling/haplotypecaller/testT/testT.haplotypecaller.vcf.gz.tbi" + ], + [ + "bcftools-stats-subtypes.txt:md5,698ccfbefaf3aa88da0ae8bceaf2bc87", + "bcftools_stats_indel-lengths.txt:md5,200444329f3f9392f299c61fbe9296b0", + "bcftools_stats_variant_depths.txt:md5,22cf631a39ef288c9e6c9facc68a61c6", + "bcftools_stats_vqc_Count_Indels.txt:md5,e372c4546a725d323f4a4350aa148ea0", + "bcftools_stats_vqc_Count_SNP.txt:md5,87e178164b6ed20014cd97d5590b64ab", + "bcftools_stats_vqc_Count_Transitions.txt:md5,20c63ab88b2e368bd958e6cdd1487855", + "bcftools_stats_vqc_Count_Transversions.txt:md5,754dfc24818b07f584fb0f205aaad50d", + "multiqc_bcftools_stats.txt:md5,3769bb9010628ee799d088bfd9c60662", + "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", + "vcftools_tstv_by_count.txt:md5,c58d953b253b5ba4d65da093064e5fd5", + "testN.freebayes.bcftools_stats.txt:md5,a4314ea6434629bae54b288f54f0c3bc", + "testT.freebayes.bcftools_stats.txt:md5,62b05f3f02d3d3f92bd57f2f813feb7b", + "testN.haplotypecaller.filtered.bcftools_stats.txt:md5,c6ae8e784f8d1550e0b49bb1cfe3128c", + "testT.haplotypecaller.filtered.bcftools_stats.txt:md5,03057e323dfc1dda8dea8a72a43fff9c", + "testN.recal.mosdepth.global.dist.txt:md5,bdb8f185c35dd1eec7ce2f69bce57972", + "testN.recal.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2", + "testN.recal.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40", + "testN.recal.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e", + "testN.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d", + "testT.recal.mosdepth.global.dist.txt:md5,3106c114529adc4231badeb3bb38b6d1", + "testT.recal.mosdepth.region.dist.txt:md5,ccf646922b05cb4759c4f89072be2b69", + "testT.recal.mosdepth.summary.txt:md5,024649a659caff330dfbef4ac3560542", + "testT.recal.regions.bed.gz:md5,14b36a2cf428840aab471f95cfbe399f", + "testT.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d", + "testN.recal.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac", + "testT.recal.cram.stats:md5,fae549c0c944f6cc34dd6d9b9569e3d3", + "testN.freebayes.FILTER.summary:md5,2ec507a210cf7de0425b6c8028a6edf8", + "testN.freebayes.TsTv.count:md5,4913577b275634ea33077dd023325dee", + "testT.freebayes.FILTER.summary:md5,50f90bd0cdd1e95c10d7e5d88d0346f8", + "testT.freebayes.TsTv.count:md5,7dba80ae65355e64a4d2d8a100db822b", + "testN.haplotypecaller.filtered.FILTER.summary:md5,4e2ceea7f3ff998004691fd71192d9ee", + "testN.haplotypecaller.filtered.TsTv.count:md5,b77c120ee5cc0423267200c67d60c663", + "testT.haplotypecaller.filtered.FILTER.summary:md5,bedf7a690b985e8ff74eef9f4c1a8c34", + "testT.haplotypecaller.filtered.TsTv.count:md5,803d74e40f7716202bae2a3a81c1ddfc", + "versions.yml:md5,69c573f208c12410e6a0ec7059a0f24e", + "versions.yml:md5,69c573f208c12410e6a0ec7059a0f24e" + ], + [ + [ + "testN.germline.vcf.gz", + "722f25aa13e7b6f34e8fff98202495cb" + ], + [ + "testT.germline.vcf.gz", + "ba2aba068afc37bf3a973b188b2c4bcc" + ], + [ + "testN.freebayes.vcf.gz", + "1d98e39fe458af9020283de18c764055" + ], + [ + "testT.freebayes.vcf.gz", + "387b7d48d04ad3b294f07173e6550fc7" + ], + [ + "testN.haplotypecaller.filtered.vcf.gz", + "df2040bf1bee0252581824d11d5d87d1" + ], + [ + "testN.haplotypecaller.vcf.gz", + "9d9d103327d59d17e778b663b56136fb" + ], + [ + "testT.haplotypecaller.filtered.vcf.gz", + "d1e2d43d91858677d2b35fc389ee81b1" + ], + [ + "testT.haplotypecaller.vcf.gz", + "5a2f49f0a41e890f9564a0baa11dc1c6" + ] + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "24.10.4" + }, + "timestamp": "2025-02-24T18:36:32.697622794" + } +} \ No newline at end of file diff --git a/tests/postprocess_normalization.nf.test b/tests/postprocess_normalization.nf.test new file mode 100644 index 0000000000..5423ea4b4d --- /dev/null +++ b/tests/postprocess_normalization.nf.test @@ -0,0 +1,46 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + tag "pipeline_sarek" + + test("-profile test --normalize_vcfs --tools freebayes,haplotypecaller") { + + when { + params { + + input = "${projectDir}/tests/csv/3.0/mapped_joint_bam.csv" + step = 'variant_calling' + normalize_vcfs = true + tools = 'freebayes,haplotypecaller' + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + } + } + + then { + // stable_name: All files + folders in ${params.outdir}/ with a stable name + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) + // stable_path: All files in ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // vcf_files: All vcf files + def vcf_files = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz']) + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"), + // All stable path name, with a relative path + stable_name, + // All files with stable contents + stable_path, + // All vcf files + vcf_files.collect { file -> [file.getName(), path(file.toString()).vcf.variantsMD5] } + ).match() } + ) + } + } +} diff --git a/tests/postprocess_normalization.nf.test.snap b/tests/postprocess_normalization.nf.test.snap new file mode 100644 index 0000000000..177eb5015e --- /dev/null +++ b/tests/postprocess_normalization.nf.test.snap @@ -0,0 +1,375 @@ +{ + "-profile test --normalize_vcfs --concatenate_vcfs --tools freebayes,haplotypecaller": { + "content": [ + 93, + { + "ADD_INFO_TO_VCF": { + "gawk": "5.1.0" + }, + "BCFTOOLS_SORT": { + "bcftools": 1.2 + }, + "BCFTOOLS_STATS": { + "bcftools": 1.2 + }, + "CNNSCOREVARIANTS": { + "gatk4": "4.5.0.0" + }, + "FILTERVARIANTTRANCHES": { + "gatk4": "4.5.0.0" + }, + "FREEBAYES": { + "freebayes": "1.3.6" + }, + "GATK4_HAPLOTYPECALLER": { + "gatk4": "4.5.0.0" + }, + "GERMLINE_VCFS_CONCAT": { + "bcftools": 1.2 + }, + "GERMLINE_VCFS_CONCAT_SORT": { + "bcftools": 1.2 + }, + "TABIX_EXT_VCF": { + "tabix": 1.2 + }, + "TABIX_GERMLINE_VCFS_CONCAT_SORT": { + "tabix": 1.2 + }, + "TABIX_VCFS_NORM_SORT": { + "tabix": 1.2 + }, + "TABIX_VC_FREEBAYES": { + "tabix": 1.2 + }, + "VCFS_NORM": { + "bcftools": 1.2 + }, + "VCFS_NORM_SORT": { + "bcftools": 1.2 + }, + "VCFTOOLS_TSTV_COUNT": { + "vcftools": "0.1.16" + }, + "Workflow": { + "nf-core/sarek": "v3.6.0dev" + } + }, + [ + "csv", + "csv/variantcalled.csv", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/bcftools-stats-subtypes.txt", + "multiqc/multiqc_data/bcftools_stats_indel-lengths.txt", + "multiqc/multiqc_data/bcftools_stats_variant_depths.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc_bcftools_stats.txt", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_data/vcftools_tstv_by_count.txt", + "multiqc/multiqc_data/vcftools_tstv_by_qual.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_variant_depths.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf", + "multiqc/multiqc_plots/pdf/general_stats_table.pdf", + "multiqc/multiqc_plots/pdf/vcftools_tstv_by_count.pdf", + "multiqc/multiqc_plots/pdf/vcftools_tstv_by_qual.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/bcftools-stats-subtypes-cnt.png", + "multiqc/multiqc_plots/png/bcftools-stats-subtypes-pct.png", + "multiqc/multiqc_plots/png/bcftools_stats_indel-lengths.png", + "multiqc/multiqc_plots/png/bcftools_stats_variant_depths.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png", + "multiqc/multiqc_plots/png/general_stats_table.png", + "multiqc/multiqc_plots/png/vcftools_tstv_by_count.png", + "multiqc/multiqc_plots/png/vcftools_tstv_by_qual.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-cnt.svg", + "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-pct.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_variant_depths.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg", + "multiqc/multiqc_plots/svg/general_stats_table.svg", + "multiqc/multiqc_plots/svg/vcftools_tstv_by_count.svg", + "multiqc/multiqc_plots/svg/vcftools_tstv_by_qual.svg", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_sarek_software_mqc_versions.yml", + "reference", + "reports", + "reports/bcftools", + "reports/bcftools/freebayes", + "reports/bcftools/freebayes/testN", + "reports/bcftools/freebayes/testN/testN.freebayes.norm.bcftools_stats.txt", + "reports/bcftools/freebayes/testN/testN.germline.bcftools_stats.txt", + "reports/bcftools/freebayes/testT", + "reports/bcftools/freebayes/testT/testT.freebayes.norm.bcftools_stats.txt", + "reports/bcftools/freebayes/testT/testT.germline.bcftools_stats.txt", + "reports/bcftools/haplotypecaller", + "reports/bcftools/haplotypecaller/testN", + "reports/bcftools/haplotypecaller/testN/testN.germline.bcftools_stats.txt", + "reports/bcftools/haplotypecaller/testN/testN.haplotypecaller.norm.bcftools_stats.txt", + "reports/bcftools/haplotypecaller/testT", + "reports/bcftools/haplotypecaller/testT/testT.germline.bcftools_stats.txt", + "reports/bcftools/haplotypecaller/testT/testT.haplotypecaller.norm.bcftools_stats.txt", + "reports/mosdepth", + "reports/mosdepth/testN", + "reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt", + "reports/mosdepth/testN/testN.recal.mosdepth.region.dist.txt", + "reports/mosdepth/testN/testN.recal.mosdepth.summary.txt", + "reports/mosdepth/testN/testN.recal.regions.bed.gz", + "reports/mosdepth/testN/testN.recal.regions.bed.gz.csi", + "reports/mosdepth/testT", + "reports/mosdepth/testT/testT.recal.mosdepth.global.dist.txt", + "reports/mosdepth/testT/testT.recal.mosdepth.region.dist.txt", + "reports/mosdepth/testT/testT.recal.mosdepth.summary.txt", + "reports/mosdepth/testT/testT.recal.regions.bed.gz", + "reports/mosdepth/testT/testT.recal.regions.bed.gz.csi", + "reports/samtools", + "reports/samtools/testN", + "reports/samtools/testN/testN.recal.cram.stats", + "reports/samtools/testT", + "reports/samtools/testT/testT.recal.cram.stats", + "reports/vcftools", + "reports/vcftools/freebayes", + "reports/vcftools/freebayes/testN", + "reports/vcftools/freebayes/testN/testN.freebayes.norm.FILTER.summary", + 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"d1e2d43d91858677d2b35fc389ee81b1" + ], + [ + "testT.haplotypecaller.vcf.gz", + "5a2f49f0a41e890f9564a0baa11dc1c6" + ], + [ + "testN.freebayes.norm.vcf.gz", + "7a4bd608db8b02c02de0393f05edf12" + ], + [ + "testN.haplotypecaller.norm.vcf.gz", + "141a2cc53b0a9d4a0ab4d779cb1e487" + ], + [ + "testN.vcf.gz", + "141a2cc53b0a9d4a0ab4d779cb1e487" + ], + [ + "testT.freebayes.norm.vcf.gz", + "7bac441a7c84790f43d26a73e10be9b5" + ], + [ + "testT.haplotypecaller.norm.vcf.gz", + "9119ee2c970c37729dcb35d4b88f9d10" + ], + [ + "testT.vcf.gz", + "9119ee2c970c37729dcb35d4b88f9d10" + ] + ] + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.01.0" + }, + "timestamp": "2025-03-03T15:21:02.272141223" + } +} \ No newline at end of file From 00940506c80910047cbb93a26c4a3ed6152a9c56 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 3 Mar 2025 16:03:19 +0100 Subject: [PATCH 02/14] CI --- .github/workflows/nf-test.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml index fd29bc1a05..14053d8fe4 100644 --- a/.github/workflows/nf-test.yml +++ b/.github/workflows/nf-test.yml @@ -5,7 +5,9 @@ on: # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging - "renovate/**" # branches Renovate creates pull_request: - branches: [dev] + branches: + - dev + - dev_normalization #TODO: remove this when merging normalization workflow_dispatch: inputs: runners: From d5f2cbee15ee067df8b4560d6ed524c326bfc34f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 3 Mar 2025 17:24:01 +0100 Subject: [PATCH 03/14] regenerate snapshots --- .../local/post_variantcalling/main.nf | 20 +- tests/postprocess_concatenation.nf.test.snap | 50 +++- ...s_concatenation_normalization.nf.test.snap | 206 ++++++++++---- tests/postprocess_normalization.nf.test.snap | 259 +----------------- 4 files changed, 218 insertions(+), 317 deletions(-) diff --git a/subworkflows/local/post_variantcalling/main.nf b/subworkflows/local/post_variantcalling/main.nf index 86bcd47353..cfd8e5b192 100644 --- a/subworkflows/local/post_variantcalling/main.nf +++ b/subworkflows/local/post_variantcalling/main.nf @@ -2,11 +2,10 @@ // POST VARIANT CALLING: processes run on variantcalled but not annotated VCFs // -include { CONCATENATE_GERMLINE_VCFS } from '../vcf_concatenate_germline/main' -include { NORMALIZE_VCFS } from '../vcf_normalization/main' +include { CONCATENATE_GERMLINE_VCFS } from '../vcf_concatenate_germline' +include { NORMALIZE_VCFS } from '../vcf_normalization' workflow POST_VARIANTCALLING { - take: germline_vcfs tumor_only_vcfs @@ -19,22 +18,29 @@ workflow POST_VARIANTCALLING { versions = Channel.empty() vcfs = Channel.empty() - if (concatenate_vcfs){ + if (concatenate_vcfs) { CONCATENATE_GERMLINE_VCFS(germline_vcfs) vcfs = vcfs.mix(CONCATENATE_GERMLINE_VCFS.out.vcfs) versions = versions.mix(CONCATENATE_GERMLINE_VCFS.out.versions) + + vcfs.view { "concat:" + it } } - if (normalize_vcfs){ + if (normalize_vcfs) { + germline_vcfs.view { "germline:" + it } + tumor_only_vcfs.view { "tumor_only:" + it } + somatic_vcfs.view { "somatic:" + it } + NORMALIZE_VCFS(germline_vcfs, tumor_only_vcfs, somatic_vcfs, fasta) vcfs = vcfs.mix(NORMALIZE_VCFS.out.vcfs) + + vcfs.view { "normalize:" + it } versions = versions.mix(NORMALIZE_VCFS.out.versions) } emit: - vcfs // post processed vcfs - + vcfs // post processed vcfs versions // channel: [ versions.yml ] } diff --git a/tests/postprocess_concatenation.nf.test.snap b/tests/postprocess_concatenation.nf.test.snap index c78d8d1539..eee85879d8 100644 --- a/tests/postprocess_concatenation.nf.test.snap +++ b/tests/postprocess_concatenation.nf.test.snap @@ -1,7 +1,7 @@ { "-profile test --concatenate_vcfs --tools freebayes,haplotypecaller": { "content": [ - 51, + 57, { "ADD_INFO_TO_VCF": { "gawk": "5.1.0" @@ -27,6 +27,9 @@ "GERMLINE_VCFS_CONCAT": { "bcftools": 1.2 }, + "GERMLINE_VCFS_CONCAT_SORT": { + "bcftools": 1.2 + }, "TABIX_EXT_VCF": { "tabix": 1.2 }, @@ -154,16 +157,23 @@ "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.filtered.FILTER.summary", "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.filtered.TsTv.count", "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.filtered.TsTv.qual", + "tabix", + "tabix/testN.freebayes.added_info.vcf.gz", + "tabix/testN.freebayes.added_info.vcf.gz.tbi", + "tabix/testN.haplotypecaller.filtered.added_info.vcf.gz", + "tabix/testN.haplotypecaller.filtered.added_info.vcf.gz.tbi", + "tabix/testT.freebayes.added_info.vcf.gz", + "tabix/testT.freebayes.added_info.vcf.gz.tbi", + "tabix/testT.haplotypecaller.filtered.added_info.vcf.gz", + "tabix/testT.haplotypecaller.filtered.added_info.vcf.gz.tbi", "variant_calling", "variant_calling/concat", "variant_calling/concat/testN", "variant_calling/concat/testN/testN.germline.vcf.gz", "variant_calling/concat/testN/testN.germline.vcf.gz.tbi", - "variant_calling/concat/testN/versions.yml", "variant_calling/concat/testT", "variant_calling/concat/testT/testT.germline.vcf.gz", "variant_calling/concat/testT/testT.germline.vcf.gz.tbi", - "variant_calling/concat/testT/versions.yml", "variant_calling/freebayes", "variant_calling/freebayes/testN", "variant_calling/freebayes/testN/testN.freebayes.vcf.gz", @@ -218,17 +228,39 @@ "testN.haplotypecaller.filtered.TsTv.count:md5,b77c120ee5cc0423267200c67d60c663", "testT.haplotypecaller.filtered.FILTER.summary:md5,bedf7a690b985e8ff74eef9f4c1a8c34", "testT.haplotypecaller.filtered.TsTv.count:md5,803d74e40f7716202bae2a3a81c1ddfc", - "versions.yml:md5,69c573f208c12410e6a0ec7059a0f24e", - "versions.yml:md5,69c573f208c12410e6a0ec7059a0f24e" + "testN.freebayes.added_info.vcf.gz:md5,3d11a31903613d6bb4ac6cb4aea5a853", + "testN.freebayes.added_info.vcf.gz.tbi:md5,0c029eab0c4f710f313d6625d3aa875a", + "testN.haplotypecaller.filtered.added_info.vcf.gz:md5,763e57fe74663dbf51edc7e9b5edf740", + "testN.haplotypecaller.filtered.added_info.vcf.gz.tbi:md5,203ece61dfe7c1741aa1081f5a6c1712", + "testT.freebayes.added_info.vcf.gz:md5,9fdc585205dbcf27bb8a43beb4a2683c", + "testT.freebayes.added_info.vcf.gz.tbi:md5,f9e6393f97e5dfb7dd07b7b852080e73", + "testT.haplotypecaller.filtered.added_info.vcf.gz:md5,274f6a55bd0a25d574d589c2cdeff457", + "testT.haplotypecaller.filtered.added_info.vcf.gz.tbi:md5,8d48dc24dd93ad4beb7fe9ee32f0829f" ], [ + [ + "testN.freebayes.added_info.vcf.gz", + "184743db45c933febc5557d08b19f23c" + ], + [ + "testN.haplotypecaller.filtered.added_info.vcf.gz", + "6070da7b2505011232eb5975d8ab74aa" + ], + [ + "testT.freebayes.added_info.vcf.gz", + "7bac441a7c84790f43d26a73e10be9b5" + ], + [ + "testT.haplotypecaller.filtered.added_info.vcf.gz", + "a5c9e658b834d70cc8cafbd94919fa4f" + ], [ "testN.germline.vcf.gz", - "722f25aa13e7b6f34e8fff98202495cb" + "184743db45c933febc5557d08b19f23c" ], [ "testT.germline.vcf.gz", - "ba2aba068afc37bf3a973b188b2c4bcc" + "7bac441a7c84790f43d26a73e10be9b5" ], [ "testN.freebayes.vcf.gz", @@ -258,8 +290,8 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-24T18:36:32.697622794" + "timestamp": "2025-03-03T17:18:33.848850992" } } \ No newline at end of file diff --git a/tests/postprocess_concatenation_normalization.nf.test.snap b/tests/postprocess_concatenation_normalization.nf.test.snap index c78d8d1539..d6c4f4b6c3 100644 --- a/tests/postprocess_concatenation_normalization.nf.test.snap +++ b/tests/postprocess_concatenation_normalization.nf.test.snap @@ -1,7 +1,7 @@ { - "-profile test --concatenate_vcfs --tools freebayes,haplotypecaller": { + "-profile test --normalize_vcfs --concatenate_vcfs --tools freebayes,haplotypecaller": { "content": [ - 51, + 93, { "ADD_INFO_TO_VCF": { "gawk": "5.1.0" @@ -27,15 +27,27 @@ "GERMLINE_VCFS_CONCAT": { "bcftools": 1.2 }, + "GERMLINE_VCFS_CONCAT_SORT": { + "bcftools": 1.2 + }, "TABIX_EXT_VCF": { "tabix": 1.2 }, "TABIX_GERMLINE_VCFS_CONCAT_SORT": { "tabix": 1.2 }, + "TABIX_VCFS_NORM_SORT": { + "tabix": 1.2 + }, "TABIX_VC_FREEBAYES": { "tabix": 1.2 }, + "VCFS_NORM": { + "bcftools": 1.2 + }, + "VCFS_NORM_SORT": { + "bcftools": 1.2 + }, "VCFTOOLS_TSTV_COUNT": { "vcftools": "0.1.16" }, @@ -109,14 +121,18 @@ "reports/bcftools", "reports/bcftools/freebayes", "reports/bcftools/freebayes/testN", - "reports/bcftools/freebayes/testN/testN.freebayes.bcftools_stats.txt", + "reports/bcftools/freebayes/testN/testN.freebayes.norm.bcftools_stats.txt", + "reports/bcftools/freebayes/testN/testN.germline.bcftools_stats.txt", "reports/bcftools/freebayes/testT", - "reports/bcftools/freebayes/testT/testT.freebayes.bcftools_stats.txt", + "reports/bcftools/freebayes/testT/testT.freebayes.norm.bcftools_stats.txt", + "reports/bcftools/freebayes/testT/testT.germline.bcftools_stats.txt", "reports/bcftools/haplotypecaller", "reports/bcftools/haplotypecaller/testN", - "reports/bcftools/haplotypecaller/testN/testN.haplotypecaller.filtered.bcftools_stats.txt", + "reports/bcftools/haplotypecaller/testN/testN.germline.bcftools_stats.txt", + "reports/bcftools/haplotypecaller/testN/testN.haplotypecaller.norm.bcftools_stats.txt", "reports/bcftools/haplotypecaller/testT", - "reports/bcftools/haplotypecaller/testT/testT.haplotypecaller.filtered.bcftools_stats.txt", + "reports/bcftools/haplotypecaller/testT/testT.germline.bcftools_stats.txt", + "reports/bcftools/haplotypecaller/testT/testT.haplotypecaller.norm.bcftools_stats.txt", "reports/mosdepth", "reports/mosdepth/testN", "reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt", @@ -138,32 +154,51 @@ "reports/vcftools", "reports/vcftools/freebayes", "reports/vcftools/freebayes/testN", - "reports/vcftools/freebayes/testN/testN.freebayes.FILTER.summary", - "reports/vcftools/freebayes/testN/testN.freebayes.TsTv.count", - "reports/vcftools/freebayes/testN/testN.freebayes.TsTv.qual", + "reports/vcftools/freebayes/testN/testN.freebayes.norm.FILTER.summary", + "reports/vcftools/freebayes/testN/testN.freebayes.norm.TsTv.count", + "reports/vcftools/freebayes/testN/testN.freebayes.norm.TsTv.qual", + "reports/vcftools/freebayes/testN/testN.germline.FILTER.summary", + "reports/vcftools/freebayes/testN/testN.germline.TsTv.count", + "reports/vcftools/freebayes/testN/testN.germline.TsTv.qual", "reports/vcftools/freebayes/testT", - "reports/vcftools/freebayes/testT/testT.freebayes.FILTER.summary", - "reports/vcftools/freebayes/testT/testT.freebayes.TsTv.count", - "reports/vcftools/freebayes/testT/testT.freebayes.TsTv.qual", + "reports/vcftools/freebayes/testT/testT.freebayes.norm.FILTER.summary", + "reports/vcftools/freebayes/testT/testT.freebayes.norm.TsTv.count", + "reports/vcftools/freebayes/testT/testT.freebayes.norm.TsTv.qual", + "reports/vcftools/freebayes/testT/testT.germline.FILTER.summary", + "reports/vcftools/freebayes/testT/testT.germline.TsTv.count", + "reports/vcftools/freebayes/testT/testT.germline.TsTv.qual", "reports/vcftools/haplotypecaller", "reports/vcftools/haplotypecaller/testN", - "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.filtered.FILTER.summary", - "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.filtered.TsTv.count", - "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.filtered.TsTv.qual", + "reports/vcftools/haplotypecaller/testN/testN.germline.FILTER.summary", + "reports/vcftools/haplotypecaller/testN/testN.germline.TsTv.count", + "reports/vcftools/haplotypecaller/testN/testN.germline.TsTv.qual", + "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.norm.FILTER.summary", + "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.norm.TsTv.count", + "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.norm.TsTv.qual", "reports/vcftools/haplotypecaller/testT", - "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.filtered.FILTER.summary", - "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.filtered.TsTv.count", - "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.filtered.TsTv.qual", + "reports/vcftools/haplotypecaller/testT/testT.germline.FILTER.summary", + "reports/vcftools/haplotypecaller/testT/testT.germline.TsTv.count", + "reports/vcftools/haplotypecaller/testT/testT.germline.TsTv.qual", + "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.norm.FILTER.summary", + "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.norm.TsTv.count", + "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.norm.TsTv.qual", + "tabix", + "tabix/testN.freebayes.added_info.vcf.gz", + "tabix/testN.freebayes.added_info.vcf.gz.tbi", + "tabix/testN.haplotypecaller.filtered.added_info.vcf.gz", + "tabix/testN.haplotypecaller.filtered.added_info.vcf.gz.tbi", + "tabix/testT.freebayes.added_info.vcf.gz", + "tabix/testT.freebayes.added_info.vcf.gz.tbi", + "tabix/testT.haplotypecaller.filtered.added_info.vcf.gz", + "tabix/testT.haplotypecaller.filtered.added_info.vcf.gz.tbi", "variant_calling", "variant_calling/concat", "variant_calling/concat/testN", "variant_calling/concat/testN/testN.germline.vcf.gz", "variant_calling/concat/testN/testN.germline.vcf.gz.tbi", - "variant_calling/concat/testN/versions.yml", "variant_calling/concat/testT", "variant_calling/concat/testT/testT.germline.vcf.gz", "variant_calling/concat/testT/testT.germline.vcf.gz.tbi", - "variant_calling/concat/testT/versions.yml", "variant_calling/freebayes", "variant_calling/freebayes/testN", "variant_calling/freebayes/testN/testN.freebayes.vcf.gz", @@ -181,23 +216,42 @@ "variant_calling/haplotypecaller/testT/testT.haplotypecaller.filtered.vcf.gz", "variant_calling/haplotypecaller/testT/testT.haplotypecaller.filtered.vcf.gz.tbi", "variant_calling/haplotypecaller/testT/testT.haplotypecaller.vcf.gz", - "variant_calling/haplotypecaller/testT/testT.haplotypecaller.vcf.gz.tbi" + "variant_calling/haplotypecaller/testT/testT.haplotypecaller.vcf.gz.tbi", + "variant_calling/normalized", + "variant_calling/normalized/testN", + "variant_calling/normalized/testN/testN.freebayes.norm.vcf.gz", + "variant_calling/normalized/testN/testN.freebayes.norm.vcf.gz.tbi", + "variant_calling/normalized/testN/testN.haplotypecaller.norm.vcf.gz", + "variant_calling/normalized/testN/testN.haplotypecaller.norm.vcf.gz.tbi", + "variant_calling/normalized/testN/testN.vcf.gz", + "variant_calling/normalized/testN/versions.yml", + "variant_calling/normalized/testT", + "variant_calling/normalized/testT/testT.freebayes.norm.vcf.gz", + "variant_calling/normalized/testT/testT.freebayes.norm.vcf.gz.tbi", + "variant_calling/normalized/testT/testT.haplotypecaller.norm.vcf.gz", + "variant_calling/normalized/testT/testT.haplotypecaller.norm.vcf.gz.tbi", + "variant_calling/normalized/testT/testT.vcf.gz", + "variant_calling/normalized/testT/versions.yml" ], [ - "bcftools-stats-subtypes.txt:md5,698ccfbefaf3aa88da0ae8bceaf2bc87", - "bcftools_stats_indel-lengths.txt:md5,200444329f3f9392f299c61fbe9296b0", - "bcftools_stats_variant_depths.txt:md5,22cf631a39ef288c9e6c9facc68a61c6", - "bcftools_stats_vqc_Count_Indels.txt:md5,e372c4546a725d323f4a4350aa148ea0", - "bcftools_stats_vqc_Count_SNP.txt:md5,87e178164b6ed20014cd97d5590b64ab", - "bcftools_stats_vqc_Count_Transitions.txt:md5,20c63ab88b2e368bd958e6cdd1487855", - "bcftools_stats_vqc_Count_Transversions.txt:md5,754dfc24818b07f584fb0f205aaad50d", - "multiqc_bcftools_stats.txt:md5,3769bb9010628ee799d088bfd9c60662", + "bcftools-stats-subtypes.txt:md5,f29bbede2599940bd8f4bd5afe62493d", + "bcftools_stats_indel-lengths.txt:md5,87f965fc8bc1f27539ce6577e79e5f36", + "bcftools_stats_variant_depths.txt:md5,74610e9ff9bdc17c8b856d4f64960e5f", + "bcftools_stats_vqc_Count_Indels.txt:md5,6c625cd035db437502b4fc563d0b858a", + "bcftools_stats_vqc_Count_SNP.txt:md5,e5f7554922f9a39d7f9e76684d2c53c1", + "bcftools_stats_vqc_Count_Transitions.txt:md5,b0925dfbbcdcd19b8c791fbf365f08e7", + "bcftools_stats_vqc_Count_Transversions.txt:md5,b9cea64a8c6379c612bb6fc437230a04", + "multiqc_bcftools_stats.txt:md5,f89d57210865bd13c25956350add2112", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", - "vcftools_tstv_by_count.txt:md5,c58d953b253b5ba4d65da093064e5fd5", - "testN.freebayes.bcftools_stats.txt:md5,a4314ea6434629bae54b288f54f0c3bc", - "testT.freebayes.bcftools_stats.txt:md5,62b05f3f02d3d3f92bd57f2f813feb7b", - "testN.haplotypecaller.filtered.bcftools_stats.txt:md5,c6ae8e784f8d1550e0b49bb1cfe3128c", - "testT.haplotypecaller.filtered.bcftools_stats.txt:md5,03057e323dfc1dda8dea8a72a43fff9c", + "vcftools_tstv_by_count.txt:md5,9f5ebe521f42a6d16269f1ada5cbe1e5", + "testN.freebayes.norm.bcftools_stats.txt:md5,1cadbd27bb650441dadfd6984e44190f", + "testN.germline.bcftools_stats.txt:md5,b8a3832c78fad6f4a182ea2a51fc82c3", + "testT.freebayes.norm.bcftools_stats.txt:md5,2ea5c1d5a877254d4807cc6a82c23f43", + "testT.germline.bcftools_stats.txt:md5,38218ede728ead2196270fdaf71e3d6b", + "testN.germline.bcftools_stats.txt:md5,4a8cdfb69f76ccd4f90603ff7e189cd2", + "testN.haplotypecaller.norm.bcftools_stats.txt:md5,2d71e5e97bac8219bb6284d50d6b1e96", + "testT.germline.bcftools_stats.txt:md5,5d8a645e1edf0d37d869578c8f3e3535", + "testT.haplotypecaller.norm.bcftools_stats.txt:md5,dc1c032230e6b9c67358475f50e0eb37", "testN.recal.mosdepth.global.dist.txt:md5,bdb8f185c35dd1eec7ce2f69bce57972", "testN.recal.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2", "testN.recal.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40", @@ -210,25 +264,57 @@ "testT.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d", "testN.recal.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac", "testT.recal.cram.stats:md5,fae549c0c944f6cc34dd6d9b9569e3d3", - "testN.freebayes.FILTER.summary:md5,2ec507a210cf7de0425b6c8028a6edf8", - "testN.freebayes.TsTv.count:md5,4913577b275634ea33077dd023325dee", - "testT.freebayes.FILTER.summary:md5,50f90bd0cdd1e95c10d7e5d88d0346f8", - "testT.freebayes.TsTv.count:md5,7dba80ae65355e64a4d2d8a100db822b", - "testN.haplotypecaller.filtered.FILTER.summary:md5,4e2ceea7f3ff998004691fd71192d9ee", - "testN.haplotypecaller.filtered.TsTv.count:md5,b77c120ee5cc0423267200c67d60c663", - "testT.haplotypecaller.filtered.FILTER.summary:md5,bedf7a690b985e8ff74eef9f4c1a8c34", - "testT.haplotypecaller.filtered.TsTv.count:md5,803d74e40f7716202bae2a3a81c1ddfc", - "versions.yml:md5,69c573f208c12410e6a0ec7059a0f24e", - "versions.yml:md5,69c573f208c12410e6a0ec7059a0f24e" + "testN.freebayes.norm.FILTER.summary:md5,d621a188425df0da8babce002e2f34dc", + "testN.freebayes.norm.TsTv.count:md5,232bb44db986854d3992bda0df08f54b", + "testN.germline.FILTER.summary:md5,2ec507a210cf7de0425b6c8028a6edf8", + "testN.germline.TsTv.count:md5,4913577b275634ea33077dd023325dee", + "testT.freebayes.norm.FILTER.summary:md5,50f90bd0cdd1e95c10d7e5d88d0346f8", + "testT.freebayes.norm.TsTv.count:md5,7dba80ae65355e64a4d2d8a100db822b", + "testT.germline.FILTER.summary:md5,50f90bd0cdd1e95c10d7e5d88d0346f8", + "testT.germline.TsTv.count:md5,7dba80ae65355e64a4d2d8a100db822b", + "testN.germline.FILTER.summary:md5,4e2ceea7f3ff998004691fd71192d9ee", + "testN.germline.TsTv.count:md5,b77c120ee5cc0423267200c67d60c663", + "testN.haplotypecaller.norm.FILTER.summary:md5,4e2ceea7f3ff998004691fd71192d9ee", + "testN.haplotypecaller.norm.TsTv.count:md5,b77c120ee5cc0423267200c67d60c663", + "testT.germline.FILTER.summary:md5,bedf7a690b985e8ff74eef9f4c1a8c34", + "testT.germline.TsTv.count:md5,803d74e40f7716202bae2a3a81c1ddfc", + "testT.haplotypecaller.norm.FILTER.summary:md5,bedf7a690b985e8ff74eef9f4c1a8c34", + "testT.haplotypecaller.norm.TsTv.count:md5,803d74e40f7716202bae2a3a81c1ddfc", + "testN.freebayes.added_info.vcf.gz:md5,3d11a31903613d6bb4ac6cb4aea5a853", + "testN.freebayes.added_info.vcf.gz.tbi:md5,0c029eab0c4f710f313d6625d3aa875a", + "testN.haplotypecaller.filtered.added_info.vcf.gz:md5,5cd4a5f906fd3cbfb62540d807baad79", + "testN.haplotypecaller.filtered.added_info.vcf.gz.tbi:md5,be46cc4853ffacc35f9a042984d47c3b", + "testT.freebayes.added_info.vcf.gz:md5,9fdc585205dbcf27bb8a43beb4a2683c", + "testT.freebayes.added_info.vcf.gz.tbi:md5,f9e6393f97e5dfb7dd07b7b852080e73", + "testT.haplotypecaller.filtered.added_info.vcf.gz:md5,6e5b5ffcd4b1715c859d7e9d8bf8a178", + "testT.haplotypecaller.filtered.added_info.vcf.gz.tbi:md5,17e5520e0995a8d44374791bb544d948", + "versions.yml:md5,7b0164f473a98fe0f8f097ae49c0e597", + "versions.yml:md5,7b0164f473a98fe0f8f097ae49c0e597" ], [ + [ + "testN.freebayes.added_info.vcf.gz", + "184743db45c933febc5557d08b19f23c" + ], + [ + "testN.haplotypecaller.filtered.added_info.vcf.gz", + "6070da7b2505011232eb5975d8ab74aa" + ], + [ + "testT.freebayes.added_info.vcf.gz", + "7bac441a7c84790f43d26a73e10be9b5" + ], + [ + "testT.haplotypecaller.filtered.added_info.vcf.gz", + "a5c9e658b834d70cc8cafbd94919fa4f" + ], [ "testN.germline.vcf.gz", - "722f25aa13e7b6f34e8fff98202495cb" + "141a2cc53b0a9d4a0ab4d779cb1e487" ], [ "testT.germline.vcf.gz", - "ba2aba068afc37bf3a973b188b2c4bcc" + "7bac441a7c84790f43d26a73e10be9b5" ], [ "testN.freebayes.vcf.gz", @@ -253,13 +339,37 @@ [ "testT.haplotypecaller.vcf.gz", "5a2f49f0a41e890f9564a0baa11dc1c6" + ], + [ + "testN.freebayes.norm.vcf.gz", + "7a4bd608db8b02c02de0393f05edf12" + ], + [ + "testN.haplotypecaller.norm.vcf.gz", + "141a2cc53b0a9d4a0ab4d779cb1e487" + ], + [ + "testN.vcf.gz", + "141a2cc53b0a9d4a0ab4d779cb1e487" + ], + [ + "testT.freebayes.norm.vcf.gz", + "7bac441a7c84790f43d26a73e10be9b5" + ], + [ + "testT.haplotypecaller.norm.vcf.gz", + "9119ee2c970c37729dcb35d4b88f9d10" + ], + [ + "testT.vcf.gz", + "9119ee2c970c37729dcb35d4b88f9d10" ] ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-24T18:36:32.697622794" + "timestamp": "2025-03-03T17:21:03.992331653" } } \ No newline at end of file diff --git a/tests/postprocess_normalization.nf.test.snap b/tests/postprocess_normalization.nf.test.snap index 177eb5015e..6b5c258b5d 100644 --- a/tests/postprocess_normalization.nf.test.snap +++ b/tests/postprocess_normalization.nf.test.snap @@ -1,17 +1,11 @@ { - "-profile test --normalize_vcfs --concatenate_vcfs --tools freebayes,haplotypecaller": { + "-profile test --normalize_vcfs --tools freebayes,haplotypecaller": { "content": [ - 93, + 21, { - "ADD_INFO_TO_VCF": { - "gawk": "5.1.0" - }, "BCFTOOLS_SORT": { "bcftools": 1.2 }, - "BCFTOOLS_STATS": { - "bcftools": 1.2 - }, "CNNSCOREVARIANTS": { "gatk4": "4.5.0.0" }, @@ -24,115 +18,27 @@ "GATK4_HAPLOTYPECALLER": { "gatk4": "4.5.0.0" }, - "GERMLINE_VCFS_CONCAT": { - "bcftools": 1.2 - }, - "GERMLINE_VCFS_CONCAT_SORT": { - "bcftools": 1.2 - }, - "TABIX_EXT_VCF": { - "tabix": 1.2 - }, - "TABIX_GERMLINE_VCFS_CONCAT_SORT": { - "tabix": 1.2 - }, - "TABIX_VCFS_NORM_SORT": { - "tabix": 1.2 - }, "TABIX_VC_FREEBAYES": { "tabix": 1.2 }, - "VCFS_NORM": { - "bcftools": 1.2 - }, - "VCFS_NORM_SORT": { - "bcftools": 1.2 - }, - "VCFTOOLS_TSTV_COUNT": { - "vcftools": "0.1.16" - }, "Workflow": { "nf-core/sarek": "v3.6.0dev" } }, [ "csv", - "csv/variantcalled.csv", "multiqc", "multiqc/multiqc_data", - "multiqc/multiqc_data/bcftools-stats-subtypes.txt", - "multiqc/multiqc_data/bcftools_stats_indel-lengths.txt", - "multiqc/multiqc_data/bcftools_stats_variant_depths.txt", - "multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt", - "multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt", - "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt", - "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt", "multiqc/multiqc_data/multiqc.log", - "multiqc/multiqc_data/multiqc_bcftools_stats.txt", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", - "multiqc/multiqc_data/multiqc_general_stats.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_data/vcftools_tstv_by_count.txt", - "multiqc/multiqc_data/vcftools_tstv_by_qual.txt", - "multiqc/multiqc_plots", - "multiqc/multiqc_plots/pdf", - "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf", - "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf", - "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths.pdf", - "multiqc/multiqc_plots/pdf/bcftools_stats_variant_depths.pdf", - "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf", - "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf", - "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf", - "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf", - "multiqc/multiqc_plots/pdf/general_stats_table.pdf", - "multiqc/multiqc_plots/pdf/vcftools_tstv_by_count.pdf", - "multiqc/multiqc_plots/pdf/vcftools_tstv_by_qual.pdf", - "multiqc/multiqc_plots/png", - "multiqc/multiqc_plots/png/bcftools-stats-subtypes-cnt.png", - "multiqc/multiqc_plots/png/bcftools-stats-subtypes-pct.png", - "multiqc/multiqc_plots/png/bcftools_stats_indel-lengths.png", - "multiqc/multiqc_plots/png/bcftools_stats_variant_depths.png", - "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png", - "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png", - "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png", - "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png", - "multiqc/multiqc_plots/png/general_stats_table.png", - "multiqc/multiqc_plots/png/vcftools_tstv_by_count.png", - "multiqc/multiqc_plots/png/vcftools_tstv_by_qual.png", - "multiqc/multiqc_plots/svg", - "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-cnt.svg", - "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-pct.svg", - "multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths.svg", - "multiqc/multiqc_plots/svg/bcftools_stats_variant_depths.svg", - "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg", - "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg", - "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg", - "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg", - "multiqc/multiqc_plots/svg/general_stats_table.svg", - "multiqc/multiqc_plots/svg/vcftools_tstv_by_count.svg", - "multiqc/multiqc_plots/svg/vcftools_tstv_by_qual.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_sarek_software_mqc_versions.yml", "reference", "reports", - "reports/bcftools", - "reports/bcftools/freebayes", - "reports/bcftools/freebayes/testN", - "reports/bcftools/freebayes/testN/testN.freebayes.norm.bcftools_stats.txt", - "reports/bcftools/freebayes/testN/testN.germline.bcftools_stats.txt", - "reports/bcftools/freebayes/testT", - "reports/bcftools/freebayes/testT/testT.freebayes.norm.bcftools_stats.txt", - "reports/bcftools/freebayes/testT/testT.germline.bcftools_stats.txt", - "reports/bcftools/haplotypecaller", - "reports/bcftools/haplotypecaller/testN", - "reports/bcftools/haplotypecaller/testN/testN.germline.bcftools_stats.txt", - "reports/bcftools/haplotypecaller/testN/testN.haplotypecaller.norm.bcftools_stats.txt", - "reports/bcftools/haplotypecaller/testT", - "reports/bcftools/haplotypecaller/testT/testT.germline.bcftools_stats.txt", - "reports/bcftools/haplotypecaller/testT/testT.haplotypecaller.norm.bcftools_stats.txt", "reports/mosdepth", "reports/mosdepth/testN", "reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt", @@ -151,54 +57,7 @@ "reports/samtools/testN/testN.recal.cram.stats", "reports/samtools/testT", "reports/samtools/testT/testT.recal.cram.stats", - "reports/vcftools", - "reports/vcftools/freebayes", - "reports/vcftools/freebayes/testN", - "reports/vcftools/freebayes/testN/testN.freebayes.norm.FILTER.summary", - "reports/vcftools/freebayes/testN/testN.freebayes.norm.TsTv.count", - "reports/vcftools/freebayes/testN/testN.freebayes.norm.TsTv.qual", - "reports/vcftools/freebayes/testN/testN.germline.FILTER.summary", - "reports/vcftools/freebayes/testN/testN.germline.TsTv.count", - "reports/vcftools/freebayes/testN/testN.germline.TsTv.qual", - "reports/vcftools/freebayes/testT", - "reports/vcftools/freebayes/testT/testT.freebayes.norm.FILTER.summary", - "reports/vcftools/freebayes/testT/testT.freebayes.norm.TsTv.count", - "reports/vcftools/freebayes/testT/testT.freebayes.norm.TsTv.qual", - "reports/vcftools/freebayes/testT/testT.germline.FILTER.summary", - "reports/vcftools/freebayes/testT/testT.germline.TsTv.count", - "reports/vcftools/freebayes/testT/testT.germline.TsTv.qual", - "reports/vcftools/haplotypecaller", - "reports/vcftools/haplotypecaller/testN", - "reports/vcftools/haplotypecaller/testN/testN.germline.FILTER.summary", - "reports/vcftools/haplotypecaller/testN/testN.germline.TsTv.count", - "reports/vcftools/haplotypecaller/testN/testN.germline.TsTv.qual", - "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.norm.FILTER.summary", - "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.norm.TsTv.count", - "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.norm.TsTv.qual", - "reports/vcftools/haplotypecaller/testT", - "reports/vcftools/haplotypecaller/testT/testT.germline.FILTER.summary", - "reports/vcftools/haplotypecaller/testT/testT.germline.TsTv.count", - "reports/vcftools/haplotypecaller/testT/testT.germline.TsTv.qual", - "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.norm.FILTER.summary", - "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.norm.TsTv.count", - "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.norm.TsTv.qual", - "tabix", - "tabix/testN.freebayes.added_info.vcf.gz", - "tabix/testN.freebayes.added_info.vcf.gz.tbi", - "tabix/testN.haplotypecaller.filtered.added_info.vcf.gz", - "tabix/testN.haplotypecaller.filtered.added_info.vcf.gz.tbi", - "tabix/testT.freebayes.added_info.vcf.gz", - "tabix/testT.freebayes.added_info.vcf.gz.tbi", - "tabix/testT.haplotypecaller.filtered.added_info.vcf.gz", - "tabix/testT.haplotypecaller.filtered.added_info.vcf.gz.tbi", "variant_calling", - "variant_calling/concat", - "variant_calling/concat/testN", - "variant_calling/concat/testN/testN.germline.vcf.gz", - "variant_calling/concat/testN/testN.germline.vcf.gz.tbi", - "variant_calling/concat/testT", - "variant_calling/concat/testT/testT.germline.vcf.gz", - "variant_calling/concat/testT/testT.germline.vcf.gz.tbi", "variant_calling/freebayes", "variant_calling/freebayes/testN", "variant_calling/freebayes/testN/testN.freebayes.vcf.gz", @@ -216,42 +75,10 @@ "variant_calling/haplotypecaller/testT/testT.haplotypecaller.filtered.vcf.gz", "variant_calling/haplotypecaller/testT/testT.haplotypecaller.filtered.vcf.gz.tbi", "variant_calling/haplotypecaller/testT/testT.haplotypecaller.vcf.gz", - "variant_calling/haplotypecaller/testT/testT.haplotypecaller.vcf.gz.tbi", - "variant_calling/normalized", - "variant_calling/normalized/testN", - "variant_calling/normalized/testN/testN.freebayes.norm.vcf.gz", - "variant_calling/normalized/testN/testN.freebayes.norm.vcf.gz.tbi", - "variant_calling/normalized/testN/testN.haplotypecaller.norm.vcf.gz", - "variant_calling/normalized/testN/testN.haplotypecaller.norm.vcf.gz.tbi", - "variant_calling/normalized/testN/testN.vcf.gz", - "variant_calling/normalized/testN/versions.yml", - "variant_calling/normalized/testT", - "variant_calling/normalized/testT/testT.freebayes.norm.vcf.gz", - "variant_calling/normalized/testT/testT.freebayes.norm.vcf.gz.tbi", - "variant_calling/normalized/testT/testT.haplotypecaller.norm.vcf.gz", - "variant_calling/normalized/testT/testT.haplotypecaller.norm.vcf.gz.tbi", - "variant_calling/normalized/testT/testT.vcf.gz", - "variant_calling/normalized/testT/versions.yml" + "variant_calling/haplotypecaller/testT/testT.haplotypecaller.vcf.gz.tbi" ], [ - "bcftools-stats-subtypes.txt:md5,3010ce89a93d1db389049038005f8706", - "bcftools_stats_indel-lengths.txt:md5,87f965fc8bc1f27539ce6577e79e5f36", - "bcftools_stats_variant_depths.txt:md5,8f114f73ddec1d44f8a48df71c7765fa", - "bcftools_stats_vqc_Count_Indels.txt:md5,0c2995d28e8aafb7240a378dfcd84005", - "bcftools_stats_vqc_Count_SNP.txt:md5,63949e4d74ee1ec0a37ba0fc05dc0208", - "bcftools_stats_vqc_Count_Transitions.txt:md5,f626d6e1254edb8e352e429b6a142ee0", - "bcftools_stats_vqc_Count_Transversions.txt:md5,b16c470d636d6cbea74cc8e736810f7d", - "multiqc_bcftools_stats.txt:md5,9f8b286d4679bf9920dcc9379752b480", - "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", - "vcftools_tstv_by_count.txt:md5,9f5ebe521f42a6d16269f1ada5cbe1e5", - "testN.freebayes.norm.bcftools_stats.txt:md5,1cadbd27bb650441dadfd6984e44190f", - "testN.germline.bcftools_stats.txt:md5,b8a3832c78fad6f4a182ea2a51fc82c3", - "testT.freebayes.norm.bcftools_stats.txt:md5,2ea5c1d5a877254d4807cc6a82c23f43", - "testT.germline.bcftools_stats.txt:md5,38218ede728ead2196270fdaf71e3d6b", - "testN.germline.bcftools_stats.txt:md5,4a8cdfb69f76ccd4f90603ff7e189cd2", - "testN.haplotypecaller.norm.bcftools_stats.txt:md5,2d71e5e97bac8219bb6284d50d6b1e96", - "testT.germline.bcftools_stats.txt:md5,5d8a645e1edf0d37d869578c8f3e3535", - "testT.haplotypecaller.norm.bcftools_stats.txt:md5,dc1c032230e6b9c67358475f50e0eb37", + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", "testN.recal.mosdepth.global.dist.txt:md5,bdb8f185c35dd1eec7ce2f69bce57972", "testN.recal.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2", "testN.recal.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40", @@ -263,59 +90,9 @@ "testT.recal.regions.bed.gz:md5,14b36a2cf428840aab471f95cfbe399f", "testT.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d", "testN.recal.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac", - "testT.recal.cram.stats:md5,fae549c0c944f6cc34dd6d9b9569e3d3", - "testN.freebayes.norm.FILTER.summary:md5,d621a188425df0da8babce002e2f34dc", - "testN.freebayes.norm.TsTv.count:md5,232bb44db986854d3992bda0df08f54b", - "testN.germline.FILTER.summary:md5,2ec507a210cf7de0425b6c8028a6edf8", - "testN.germline.TsTv.count:md5,4913577b275634ea33077dd023325dee", - "testT.freebayes.norm.FILTER.summary:md5,50f90bd0cdd1e95c10d7e5d88d0346f8", - "testT.freebayes.norm.TsTv.count:md5,7dba80ae65355e64a4d2d8a100db822b", - "testT.germline.FILTER.summary:md5,50f90bd0cdd1e95c10d7e5d88d0346f8", - "testT.germline.TsTv.count:md5,7dba80ae65355e64a4d2d8a100db822b", - "testN.germline.FILTER.summary:md5,4e2ceea7f3ff998004691fd71192d9ee", - "testN.germline.TsTv.count:md5,b77c120ee5cc0423267200c67d60c663", - "testN.haplotypecaller.norm.FILTER.summary:md5,4e2ceea7f3ff998004691fd71192d9ee", - "testN.haplotypecaller.norm.TsTv.count:md5,b77c120ee5cc0423267200c67d60c663", - "testT.germline.FILTER.summary:md5,bedf7a690b985e8ff74eef9f4c1a8c34", - "testT.germline.TsTv.count:md5,803d74e40f7716202bae2a3a81c1ddfc", - "testT.haplotypecaller.norm.FILTER.summary:md5,bedf7a690b985e8ff74eef9f4c1a8c34", - "testT.haplotypecaller.norm.TsTv.count:md5,803d74e40f7716202bae2a3a81c1ddfc", - "testN.freebayes.added_info.vcf.gz:md5,3d11a31903613d6bb4ac6cb4aea5a853", - "testN.freebayes.added_info.vcf.gz.tbi:md5,0c029eab0c4f710f313d6625d3aa875a", - "testN.haplotypecaller.filtered.added_info.vcf.gz:md5,fa3efb64bffcc81ce8680e2ff24f9a26", - "testN.haplotypecaller.filtered.added_info.vcf.gz.tbi:md5,8dd22496c50d5322a3730d133f0a5355", - "testT.freebayes.added_info.vcf.gz:md5,9fdc585205dbcf27bb8a43beb4a2683c", - "testT.freebayes.added_info.vcf.gz.tbi:md5,f9e6393f97e5dfb7dd07b7b852080e73", - "testT.haplotypecaller.filtered.added_info.vcf.gz:md5,5e16ce6594b22fdd3230df6acecb78dd", - "testT.haplotypecaller.filtered.added_info.vcf.gz.tbi:md5,36c6392f03a865f55b65b02182558571", - "versions.yml:md5,7b0164f473a98fe0f8f097ae49c0e597", - "versions.yml:md5,7b0164f473a98fe0f8f097ae49c0e597" + "testT.recal.cram.stats:md5,fae549c0c944f6cc34dd6d9b9569e3d3" ], [ - [ - "testN.freebayes.added_info.vcf.gz", - "184743db45c933febc5557d08b19f23c" - ], - [ - "testN.haplotypecaller.filtered.added_info.vcf.gz", - "6070da7b2505011232eb5975d8ab74aa" - ], - [ - "testT.freebayes.added_info.vcf.gz", - "7bac441a7c84790f43d26a73e10be9b5" - ], - [ - "testT.haplotypecaller.filtered.added_info.vcf.gz", - "a5c9e658b834d70cc8cafbd94919fa4f" - ], - [ - "testN.germline.vcf.gz", - "184743db45c933febc5557d08b19f23c" - ], - [ - "testT.germline.vcf.gz", - "9119ee2c970c37729dcb35d4b88f9d10" - ], [ "testN.freebayes.vcf.gz", "1d98e39fe458af9020283de18c764055" @@ -339,30 +116,6 @@ [ "testT.haplotypecaller.vcf.gz", "5a2f49f0a41e890f9564a0baa11dc1c6" - ], - [ - "testN.freebayes.norm.vcf.gz", - "7a4bd608db8b02c02de0393f05edf12" - ], - [ - "testN.haplotypecaller.norm.vcf.gz", - "141a2cc53b0a9d4a0ab4d779cb1e487" - ], - [ - "testN.vcf.gz", - "141a2cc53b0a9d4a0ab4d779cb1e487" - ], - [ - "testT.freebayes.norm.vcf.gz", - "7bac441a7c84790f43d26a73e10be9b5" - ], - [ - "testT.haplotypecaller.norm.vcf.gz", - "9119ee2c970c37729dcb35d4b88f9d10" - ], - [ - "testT.vcf.gz", - "9119ee2c970c37729dcb35d4b88f9d10" ] ] ], @@ -370,6 +123,6 @@ "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-03-03T15:21:02.272141223" + "timestamp": "2025-03-03T17:22:51.50445159" } } \ No newline at end of file From 6e7387a4d42154bdfc74999974b7d74095a49c9c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 3 Mar 2025 18:31:44 +0100 Subject: [PATCH 04/14] fix and regenerate tests --- CHANGELOG.md | 2 + conf/modules/post_variant_calling.config | 13 +- .../local/post_variantcalling/main.nf | 3 - subworkflows/local/vcf_normalization/main.nf | 18 +- tests/postprocess_concatenation.nf.test.snap | 41 +---- ...s_concatenation_normalization.nf.test.snap | 55 ++---- tests/postprocess_normalization.nf.test.snap | 172 +++++++++++++++++- 7 files changed, 199 insertions(+), 105 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 41e124446a..26503ebbd8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -39,6 +39,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1803](https://github.com/nf-core/sarek/pull/1803) - Back to dev - [1806](https://github.com/nf-core/sarek/pull/1806) - Use `nft-vcf` for nf-test vcf assertions - [1814](https://github.com/nf-core/sarek/pull/1814) - Added link to Bluesky +- [1815](https://github.com/nf-core/sarek/pull/1815) - Create nf-test pipeline pytest vcf concatenation + normalize tests #### Changed @@ -47,6 +48,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1809](https://github.com/nf-core/sarek/pull/1809) - Replace `getReadsMD5()` by `readsMD5` from `nft-bam` plugin for more global cohesion with usage of `nft-vcf` plugin - [1810](https://github.com/nf-core/sarek/pull/1810) - Implement automatic sharding for nf-test tests - [1810](https://github.com/nf-core/sarek/pull/1810) - Skip all CI but linting on docs changes +- [1815](https://github.com/nf-core/sarek/pull/1815) - Migrate pipeline pytest vcf normalize tests to nf-test #### Fixed diff --git a/conf/modules/post_variant_calling.config b/conf/modules/post_variant_calling.config index 621394cdfd..e88a4b8362 100644 --- a/conf/modules/post_variant_calling.config +++ b/conf/modules/post_variant_calling.config @@ -22,8 +22,8 @@ process { publishDir = [ enabled: false ] } - withName: 'ADD_INFO_TO_VCF'{ - ext.when = { params.concatenate_vcfs } + withName: 'ADD_INFO_TO_VCF' { + ext.when = { params.concatenate_vcfs || params.normalize_vcfs } publishDir = [ enabled: false ] } @@ -49,8 +49,8 @@ process { withName: 'VCFS_NORM' { ext.args = { [ - '--multiallelics -both', //split multiallelic sites into biallelic records and both SNPs and indels should be merged separately into two records - '--rm-dup all' //output only the first instance of a record which is present multiple times + '--multiallelics -both', // split multiallelic sites into biallelic records and both SNPs and indels should be merged separately into two records + '--rm-dup all' // output only the first instance of a record which is present multiple times ].join(' ') } ext.when = { params.normalize_vcfs } publishDir = [ @@ -62,9 +62,10 @@ process { withName: 'TABIX_EXT_VCF' { ext.prefix = { "${input.baseName}" } ext.when = { params.concatenate_vcfs || params.normalize_vcfs } + publishDir = [ enabled: false ] } - withName: 'TABIX_GERMLINE_VCFS_CONCAT_SORT'{ + withName: 'TABIX_GERMLINE_VCFS_CONCAT_SORT' { ext.prefix = { "${meta.id}.germline" } ext.when = { params.concatenate_vcfs } publishDir = [ @@ -74,7 +75,7 @@ process { ] } - withName: 'TABIX_VCFS_NORM_SORT'{ + withName: 'TABIX_VCFS_NORM_SORT' { ext.prefix = { "${meta.id}.${meta.variantcaller}.norm" } ext.when = { params.normalize_vcfs } publishDir = [ diff --git a/subworkflows/local/post_variantcalling/main.nf b/subworkflows/local/post_variantcalling/main.nf index cfd8e5b192..0ad6c321c4 100644 --- a/subworkflows/local/post_variantcalling/main.nf +++ b/subworkflows/local/post_variantcalling/main.nf @@ -23,8 +23,6 @@ workflow POST_VARIANTCALLING { vcfs = vcfs.mix(CONCATENATE_GERMLINE_VCFS.out.vcfs) versions = versions.mix(CONCATENATE_GERMLINE_VCFS.out.versions) - - vcfs.view { "concat:" + it } } if (normalize_vcfs) { @@ -36,7 +34,6 @@ workflow POST_VARIANTCALLING { vcfs = vcfs.mix(NORMALIZE_VCFS.out.vcfs) - vcfs.view { "normalize:" + it } versions = versions.mix(NORMALIZE_VCFS.out.versions) } diff --git a/subworkflows/local/vcf_normalization/main.nf b/subworkflows/local/vcf_normalization/main.nf index 3e1f9edf1e..a9ac190bbb 100644 --- a/subworkflows/local/vcf_normalization/main.nf +++ b/subworkflows/local/vcf_normalization/main.nf @@ -1,15 +1,14 @@ // Normalize all unannotated VCFs // Import modules -include { ADD_INFO_TO_VCF } from '../../../modules/local/add_info_to_vcf/main' -include { TABIX_BGZIPTABIX as TABIX_EXT_VCF } from '../../../modules/nf-core/tabix/bgziptabix/main' -include { BCFTOOLS_NORM as VCFS_NORM } from '../../../modules/nf-core/bcftools/norm/main' -include { BCFTOOLS_SORT as VCFS_NORM_SORT } from '../../../modules/nf-core/bcftools/sort/main' -include { TABIX_TABIX as TABIX_VCFS_NORM_SORT } from '../../../modules/nf-core/tabix/tabix/main' +include { ADD_INFO_TO_VCF } from '../../../modules/local/add_info_to_vcf' +include { TABIX_BGZIPTABIX as TABIX_EXT_VCF } from '../../../modules/nf-core/tabix/bgziptabix' +include { BCFTOOLS_NORM as VCFS_NORM } from '../../../modules/nf-core/bcftools/norm' +include { BCFTOOLS_SORT as VCFS_NORM_SORT } from '../../../modules/nf-core/bcftools/sort' +include { TABIX_TABIX as TABIX_VCFS_NORM_SORT } from '../../../modules/nf-core/tabix/tabix' // Workflow to normalize, compress, and index VCF files workflow NORMALIZE_VCFS { - take: germline_vcfs tumor_only_vcfs @@ -38,13 +37,12 @@ workflow NORMALIZE_VCFS { // Gather versions of all tools used versions = versions.mix(ADD_INFO_TO_VCF.out.versions) - versions = versions.mix(VCFS_NORM.out.versions) versions = versions.mix(TABIX_EXT_VCF.out.versions) - versions = versions.mix(VCFS_NORM_SORT.out.versions) versions = versions.mix(TABIX_VCFS_NORM_SORT.out.versions) + versions = versions.mix(VCFS_NORM.out.versions) + versions = versions.mix(VCFS_NORM_SORT.out.versions) emit: - vcfs = VCFS_NORM_SORT.out.vcf // normalized vcfs + vcfs = VCFS_NORM_SORT.out.vcf // normalized vcfs versions // Channel: [versions.yml] } - diff --git a/tests/postprocess_concatenation.nf.test.snap b/tests/postprocess_concatenation.nf.test.snap index eee85879d8..98924d1f50 100644 --- a/tests/postprocess_concatenation.nf.test.snap +++ b/tests/postprocess_concatenation.nf.test.snap @@ -157,15 +157,6 @@ "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.filtered.FILTER.summary", "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.filtered.TsTv.count", "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.filtered.TsTv.qual", - "tabix", - "tabix/testN.freebayes.added_info.vcf.gz", - "tabix/testN.freebayes.added_info.vcf.gz.tbi", - "tabix/testN.haplotypecaller.filtered.added_info.vcf.gz", - "tabix/testN.haplotypecaller.filtered.added_info.vcf.gz.tbi", - "tabix/testT.freebayes.added_info.vcf.gz", - "tabix/testT.freebayes.added_info.vcf.gz.tbi", - "tabix/testT.haplotypecaller.filtered.added_info.vcf.gz", - "tabix/testT.haplotypecaller.filtered.added_info.vcf.gz.tbi", "variant_calling", "variant_calling/concat", "variant_calling/concat/testN", @@ -227,40 +218,16 @@ "testN.haplotypecaller.filtered.FILTER.summary:md5,4e2ceea7f3ff998004691fd71192d9ee", "testN.haplotypecaller.filtered.TsTv.count:md5,b77c120ee5cc0423267200c67d60c663", "testT.haplotypecaller.filtered.FILTER.summary:md5,bedf7a690b985e8ff74eef9f4c1a8c34", - "testT.haplotypecaller.filtered.TsTv.count:md5,803d74e40f7716202bae2a3a81c1ddfc", - "testN.freebayes.added_info.vcf.gz:md5,3d11a31903613d6bb4ac6cb4aea5a853", - "testN.freebayes.added_info.vcf.gz.tbi:md5,0c029eab0c4f710f313d6625d3aa875a", - "testN.haplotypecaller.filtered.added_info.vcf.gz:md5,763e57fe74663dbf51edc7e9b5edf740", - "testN.haplotypecaller.filtered.added_info.vcf.gz.tbi:md5,203ece61dfe7c1741aa1081f5a6c1712", - "testT.freebayes.added_info.vcf.gz:md5,9fdc585205dbcf27bb8a43beb4a2683c", - "testT.freebayes.added_info.vcf.gz.tbi:md5,f9e6393f97e5dfb7dd07b7b852080e73", - "testT.haplotypecaller.filtered.added_info.vcf.gz:md5,274f6a55bd0a25d574d589c2cdeff457", - "testT.haplotypecaller.filtered.added_info.vcf.gz.tbi:md5,8d48dc24dd93ad4beb7fe9ee32f0829f" + "testT.haplotypecaller.filtered.TsTv.count:md5,803d74e40f7716202bae2a3a81c1ddfc" ], [ - [ - "testN.freebayes.added_info.vcf.gz", - "184743db45c933febc5557d08b19f23c" - ], - [ - "testN.haplotypecaller.filtered.added_info.vcf.gz", - "6070da7b2505011232eb5975d8ab74aa" - ], - [ - "testT.freebayes.added_info.vcf.gz", - "7bac441a7c84790f43d26a73e10be9b5" - ], - [ - "testT.haplotypecaller.filtered.added_info.vcf.gz", - "a5c9e658b834d70cc8cafbd94919fa4f" - ], [ "testN.germline.vcf.gz", - "184743db45c933febc5557d08b19f23c" + "141a2cc53b0a9d4a0ab4d779cb1e487" ], [ "testT.germline.vcf.gz", - "7bac441a7c84790f43d26a73e10be9b5" + "9119ee2c970c37729dcb35d4b88f9d10" ], [ "testN.freebayes.vcf.gz", @@ -292,6 +259,6 @@ "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-03-03T17:18:33.848850992" + "timestamp": "2025-03-03T18:24:54.468039835" } } \ No newline at end of file diff --git a/tests/postprocess_concatenation_normalization.nf.test.snap b/tests/postprocess_concatenation_normalization.nf.test.snap index d6c4f4b6c3..6c0bf3a603 100644 --- a/tests/postprocess_concatenation_normalization.nf.test.snap +++ b/tests/postprocess_concatenation_normalization.nf.test.snap @@ -182,15 +182,6 @@ "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.norm.FILTER.summary", "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.norm.TsTv.count", "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.norm.TsTv.qual", - "tabix", - "tabix/testN.freebayes.added_info.vcf.gz", - "tabix/testN.freebayes.added_info.vcf.gz.tbi", - "tabix/testN.haplotypecaller.filtered.added_info.vcf.gz", - "tabix/testN.haplotypecaller.filtered.added_info.vcf.gz.tbi", - "tabix/testT.freebayes.added_info.vcf.gz", - "tabix/testT.freebayes.added_info.vcf.gz.tbi", - "tabix/testT.haplotypecaller.filtered.added_info.vcf.gz", - "tabix/testT.haplotypecaller.filtered.added_info.vcf.gz.tbi", "variant_calling", "variant_calling/concat", "variant_calling/concat/testN", @@ -234,16 +225,16 @@ "variant_calling/normalized/testT/versions.yml" ], [ - "bcftools-stats-subtypes.txt:md5,f29bbede2599940bd8f4bd5afe62493d", + "bcftools-stats-subtypes.txt:md5,bcf830fa75544b1ee9c84c8e68fe124c", "bcftools_stats_indel-lengths.txt:md5,87f965fc8bc1f27539ce6577e79e5f36", - "bcftools_stats_variant_depths.txt:md5,74610e9ff9bdc17c8b856d4f64960e5f", - "bcftools_stats_vqc_Count_Indels.txt:md5,6c625cd035db437502b4fc563d0b858a", - "bcftools_stats_vqc_Count_SNP.txt:md5,e5f7554922f9a39d7f9e76684d2c53c1", - "bcftools_stats_vqc_Count_Transitions.txt:md5,b0925dfbbcdcd19b8c791fbf365f08e7", - "bcftools_stats_vqc_Count_Transversions.txt:md5,b9cea64a8c6379c612bb6fc437230a04", - "multiqc_bcftools_stats.txt:md5,f89d57210865bd13c25956350add2112", + "bcftools_stats_variant_depths.txt:md5,8300a50a31f5ae71feaf1d8528507fb9", + "bcftools_stats_vqc_Count_Indels.txt:md5,0ef083b15189d878aed87681fc6a0422", + "bcftools_stats_vqc_Count_SNP.txt:md5,9a0e46eefc7ffa628381f0e8064f183e", + "bcftools_stats_vqc_Count_Transitions.txt:md5,e3c4a76d51aac2c8db625121c08ace11", + "bcftools_stats_vqc_Count_Transversions.txt:md5,37d9a00ecc45f57d7b8a4e9d6b0824cb", + "multiqc_bcftools_stats.txt:md5,44fb14c8a955205b78c585cc89e08846", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", - "vcftools_tstv_by_count.txt:md5,9f5ebe521f42a6d16269f1ada5cbe1e5", + "vcftools_tstv_by_count.txt:md5,e8d339b0bf0292647bc4f24c8bd8a084", "testN.freebayes.norm.bcftools_stats.txt:md5,1cadbd27bb650441dadfd6984e44190f", "testN.germline.bcftools_stats.txt:md5,b8a3832c78fad6f4a182ea2a51fc82c3", "testT.freebayes.norm.bcftools_stats.txt:md5,2ea5c1d5a877254d4807cc6a82c23f43", @@ -280,41 +271,17 @@ "testT.germline.TsTv.count:md5,803d74e40f7716202bae2a3a81c1ddfc", "testT.haplotypecaller.norm.FILTER.summary:md5,bedf7a690b985e8ff74eef9f4c1a8c34", "testT.haplotypecaller.norm.TsTv.count:md5,803d74e40f7716202bae2a3a81c1ddfc", - "testN.freebayes.added_info.vcf.gz:md5,3d11a31903613d6bb4ac6cb4aea5a853", - "testN.freebayes.added_info.vcf.gz.tbi:md5,0c029eab0c4f710f313d6625d3aa875a", - "testN.haplotypecaller.filtered.added_info.vcf.gz:md5,5cd4a5f906fd3cbfb62540d807baad79", - "testN.haplotypecaller.filtered.added_info.vcf.gz.tbi:md5,be46cc4853ffacc35f9a042984d47c3b", - "testT.freebayes.added_info.vcf.gz:md5,9fdc585205dbcf27bb8a43beb4a2683c", - "testT.freebayes.added_info.vcf.gz.tbi:md5,f9e6393f97e5dfb7dd07b7b852080e73", - "testT.haplotypecaller.filtered.added_info.vcf.gz:md5,6e5b5ffcd4b1715c859d7e9d8bf8a178", - "testT.haplotypecaller.filtered.added_info.vcf.gz.tbi:md5,17e5520e0995a8d44374791bb544d948", "versions.yml:md5,7b0164f473a98fe0f8f097ae49c0e597", "versions.yml:md5,7b0164f473a98fe0f8f097ae49c0e597" ], [ - [ - "testN.freebayes.added_info.vcf.gz", - "184743db45c933febc5557d08b19f23c" - ], - [ - "testN.haplotypecaller.filtered.added_info.vcf.gz", - "6070da7b2505011232eb5975d8ab74aa" - ], - [ - "testT.freebayes.added_info.vcf.gz", - "7bac441a7c84790f43d26a73e10be9b5" - ], - [ - "testT.haplotypecaller.filtered.added_info.vcf.gz", - "a5c9e658b834d70cc8cafbd94919fa4f" - ], [ "testN.germline.vcf.gz", - "141a2cc53b0a9d4a0ab4d779cb1e487" + "184743db45c933febc5557d08b19f23c" ], [ "testT.germline.vcf.gz", - "7bac441a7c84790f43d26a73e10be9b5" + "9119ee2c970c37729dcb35d4b88f9d10" ], [ "testN.freebayes.vcf.gz", @@ -370,6 +337,6 @@ "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-03-03T17:21:03.992331653" + "timestamp": "2025-03-03T18:26:55.378360589" } } \ No newline at end of file diff --git a/tests/postprocess_normalization.nf.test.snap b/tests/postprocess_normalization.nf.test.snap index 6b5c258b5d..83c7013e1f 100644 --- a/tests/postprocess_normalization.nf.test.snap +++ b/tests/postprocess_normalization.nf.test.snap @@ -1,11 +1,17 @@ { "-profile test --normalize_vcfs --tools freebayes,haplotypecaller": { "content": [ - 21, + 57, { + "ADD_INFO_TO_VCF": { + "gawk": "5.1.0" + }, "BCFTOOLS_SORT": { "bcftools": 1.2 }, + "BCFTOOLS_STATS": { + "bcftools": 1.2 + }, "CNNSCOREVARIANTS": { "gatk4": "4.5.0.0" }, @@ -18,27 +24,102 @@ "GATK4_HAPLOTYPECALLER": { "gatk4": "4.5.0.0" }, + "TABIX_EXT_VCF": { + "tabix": 1.2 + }, + "TABIX_VCFS_NORM_SORT": { + "tabix": 1.2 + }, "TABIX_VC_FREEBAYES": { "tabix": 1.2 }, + "VCFS_NORM": { + "bcftools": 1.2 + }, + "VCFS_NORM_SORT": { + "bcftools": 1.2 + }, + "VCFTOOLS_TSTV_COUNT": { + "vcftools": "0.1.16" + }, "Workflow": { "nf-core/sarek": "v3.6.0dev" } }, [ "csv", + "csv/variantcalled.csv", "multiqc", "multiqc/multiqc_data", + "multiqc/multiqc_data/bcftools-stats-subtypes.txt", + "multiqc/multiqc_data/bcftools_stats_indel-lengths.txt", + "multiqc/multiqc_data/bcftools_stats_variant_depths.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt", "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc_bcftools_stats.txt", "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_general_stats.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_data/vcftools_tstv_by_count.txt", + "multiqc/multiqc_data/vcftools_tstv_by_qual.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-cnt.pdf", + "multiqc/multiqc_plots/pdf/bcftools-stats-subtypes-pct.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_indel-lengths.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_variant_depths.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Indels.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_SNP.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transitions.pdf", + "multiqc/multiqc_plots/pdf/bcftools_stats_vqc_Count_Transversions.pdf", + "multiqc/multiqc_plots/pdf/general_stats_table.pdf", + "multiqc/multiqc_plots/pdf/vcftools_tstv_by_count.pdf", + "multiqc/multiqc_plots/pdf/vcftools_tstv_by_qual.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/bcftools-stats-subtypes-cnt.png", + "multiqc/multiqc_plots/png/bcftools-stats-subtypes-pct.png", + "multiqc/multiqc_plots/png/bcftools_stats_indel-lengths.png", + "multiqc/multiqc_plots/png/bcftools_stats_variant_depths.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Indels.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_SNP.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transitions.png", + "multiqc/multiqc_plots/png/bcftools_stats_vqc_Count_Transversions.png", + "multiqc/multiqc_plots/png/general_stats_table.png", + "multiqc/multiqc_plots/png/vcftools_tstv_by_count.png", + "multiqc/multiqc_plots/png/vcftools_tstv_by_qual.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-cnt.svg", + "multiqc/multiqc_plots/svg/bcftools-stats-subtypes-pct.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_indel-lengths.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_variant_depths.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Indels.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_SNP.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transitions.svg", + "multiqc/multiqc_plots/svg/bcftools_stats_vqc_Count_Transversions.svg", + "multiqc/multiqc_plots/svg/general_stats_table.svg", + "multiqc/multiqc_plots/svg/vcftools_tstv_by_count.svg", + "multiqc/multiqc_plots/svg/vcftools_tstv_by_qual.svg", "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_sarek_software_mqc_versions.yml", "reference", "reports", + "reports/bcftools", + "reports/bcftools/freebayes", + "reports/bcftools/freebayes/testN", + "reports/bcftools/freebayes/testN/testN.freebayes.norm.bcftools_stats.txt", + "reports/bcftools/freebayes/testT", + "reports/bcftools/freebayes/testT/testT.freebayes.norm.bcftools_stats.txt", + "reports/bcftools/haplotypecaller", + "reports/bcftools/haplotypecaller/testN", + "reports/bcftools/haplotypecaller/testN/testN.haplotypecaller.norm.bcftools_stats.txt", + "reports/bcftools/haplotypecaller/testT", + "reports/bcftools/haplotypecaller/testT/testT.haplotypecaller.norm.bcftools_stats.txt", "reports/mosdepth", "reports/mosdepth/testN", "reports/mosdepth/testN/testN.recal.mosdepth.global.dist.txt", @@ -57,6 +138,25 @@ "reports/samtools/testN/testN.recal.cram.stats", "reports/samtools/testT", "reports/samtools/testT/testT.recal.cram.stats", + "reports/vcftools", + "reports/vcftools/freebayes", + "reports/vcftools/freebayes/testN", + "reports/vcftools/freebayes/testN/testN.freebayes.norm.FILTER.summary", + "reports/vcftools/freebayes/testN/testN.freebayes.norm.TsTv.count", + "reports/vcftools/freebayes/testN/testN.freebayes.norm.TsTv.qual", + "reports/vcftools/freebayes/testT", + "reports/vcftools/freebayes/testT/testT.freebayes.norm.FILTER.summary", + "reports/vcftools/freebayes/testT/testT.freebayes.norm.TsTv.count", + "reports/vcftools/freebayes/testT/testT.freebayes.norm.TsTv.qual", + "reports/vcftools/haplotypecaller", + "reports/vcftools/haplotypecaller/testN", + "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.norm.FILTER.summary", + "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.norm.TsTv.count", + "reports/vcftools/haplotypecaller/testN/testN.haplotypecaller.norm.TsTv.qual", + "reports/vcftools/haplotypecaller/testT", + "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.norm.FILTER.summary", + "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.norm.TsTv.count", + "reports/vcftools/haplotypecaller/testT/testT.haplotypecaller.norm.TsTv.qual", "variant_calling", "variant_calling/freebayes", "variant_calling/freebayes/testN", @@ -75,10 +175,38 @@ "variant_calling/haplotypecaller/testT/testT.haplotypecaller.filtered.vcf.gz", "variant_calling/haplotypecaller/testT/testT.haplotypecaller.filtered.vcf.gz.tbi", "variant_calling/haplotypecaller/testT/testT.haplotypecaller.vcf.gz", - "variant_calling/haplotypecaller/testT/testT.haplotypecaller.vcf.gz.tbi" + "variant_calling/haplotypecaller/testT/testT.haplotypecaller.vcf.gz.tbi", + "variant_calling/normalized", + "variant_calling/normalized/testN", + "variant_calling/normalized/testN/testN.freebayes.norm.vcf.gz", + "variant_calling/normalized/testN/testN.freebayes.norm.vcf.gz.tbi", + "variant_calling/normalized/testN/testN.haplotypecaller.norm.vcf.gz", + "variant_calling/normalized/testN/testN.haplotypecaller.norm.vcf.gz.tbi", + "variant_calling/normalized/testN/testN.vcf.gz", + "variant_calling/normalized/testN/versions.yml", + "variant_calling/normalized/testT", + "variant_calling/normalized/testT/testT.freebayes.norm.vcf.gz", + "variant_calling/normalized/testT/testT.freebayes.norm.vcf.gz.tbi", + "variant_calling/normalized/testT/testT.haplotypecaller.norm.vcf.gz", + "variant_calling/normalized/testT/testT.haplotypecaller.norm.vcf.gz.tbi", + "variant_calling/normalized/testT/testT.vcf.gz", + "variant_calling/normalized/testT/versions.yml" ], [ - "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "bcftools-stats-subtypes.txt:md5,14d79d00d95f319c28581b24d85b979b", + "bcftools_stats_indel-lengths.txt:md5,08d99ff43492e7225fd0afe8760b3e44", + "bcftools_stats_variant_depths.txt:md5,7e039ced7052f8c44f7fc8b8fc636f70", + "bcftools_stats_vqc_Count_Indels.txt:md5,d02630d8a8e1cb4759c207558be6e737", + "bcftools_stats_vqc_Count_SNP.txt:md5,c0ee5047463d19ece2bc64de139648d7", + "bcftools_stats_vqc_Count_Transitions.txt:md5,c11a77023dd62c9c4bd29a8139f02197", + "bcftools_stats_vqc_Count_Transversions.txt:md5,ae90d8ec6ad590d88c95edc82ea9884e", + "multiqc_bcftools_stats.txt:md5,7cf61fb13b7221379888f0756d8f322e", + "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", + "vcftools_tstv_by_count.txt:md5,6c76fc304a7d346e999b584f73c19e8e", + "testN.freebayes.norm.bcftools_stats.txt:md5,1cadbd27bb650441dadfd6984e44190f", + "testT.freebayes.norm.bcftools_stats.txt:md5,2ea5c1d5a877254d4807cc6a82c23f43", + "testN.haplotypecaller.norm.bcftools_stats.txt:md5,2d71e5e97bac8219bb6284d50d6b1e96", + "testT.haplotypecaller.norm.bcftools_stats.txt:md5,dc1c032230e6b9c67358475f50e0eb37", "testN.recal.mosdepth.global.dist.txt:md5,bdb8f185c35dd1eec7ce2f69bce57972", "testN.recal.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2", "testN.recal.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40", @@ -90,7 +218,17 @@ "testT.recal.regions.bed.gz:md5,14b36a2cf428840aab471f95cfbe399f", "testT.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d", "testN.recal.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac", - "testT.recal.cram.stats:md5,fae549c0c944f6cc34dd6d9b9569e3d3" + "testT.recal.cram.stats:md5,fae549c0c944f6cc34dd6d9b9569e3d3", + "testN.freebayes.norm.FILTER.summary:md5,d621a188425df0da8babce002e2f34dc", + "testN.freebayes.norm.TsTv.count:md5,232bb44db986854d3992bda0df08f54b", + "testT.freebayes.norm.FILTER.summary:md5,50f90bd0cdd1e95c10d7e5d88d0346f8", + "testT.freebayes.norm.TsTv.count:md5,7dba80ae65355e64a4d2d8a100db822b", + "testN.haplotypecaller.norm.FILTER.summary:md5,4e2ceea7f3ff998004691fd71192d9ee", + "testN.haplotypecaller.norm.TsTv.count:md5,b77c120ee5cc0423267200c67d60c663", + "testT.haplotypecaller.norm.FILTER.summary:md5,bedf7a690b985e8ff74eef9f4c1a8c34", + "testT.haplotypecaller.norm.TsTv.count:md5,803d74e40f7716202bae2a3a81c1ddfc", + "versions.yml:md5,7b0164f473a98fe0f8f097ae49c0e597", + "versions.yml:md5,7b0164f473a98fe0f8f097ae49c0e597" ], [ [ @@ -116,6 +254,30 @@ [ "testT.haplotypecaller.vcf.gz", "5a2f49f0a41e890f9564a0baa11dc1c6" + ], + [ + "testN.freebayes.norm.vcf.gz", + "7a4bd608db8b02c02de0393f05edf12" + ], + [ + "testN.haplotypecaller.norm.vcf.gz", + "141a2cc53b0a9d4a0ab4d779cb1e487" + ], + [ + "testN.vcf.gz", + "141a2cc53b0a9d4a0ab4d779cb1e487" + ], + [ + "testT.freebayes.norm.vcf.gz", + "7bac441a7c84790f43d26a73e10be9b5" + ], + [ + "testT.haplotypecaller.norm.vcf.gz", + "9119ee2c970c37729dcb35d4b88f9d10" + ], + [ + "testT.vcf.gz", + "9119ee2c970c37729dcb35d4b88f9d10" ] ] ], @@ -123,6 +285,6 @@ "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-03-03T17:22:51.50445159" + "timestamp": "2025-03-03T18:28:42.107225989" } } \ No newline at end of file From d7f3782aa2c6900e4345df6c63bba9d9e892a10c Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 3 Mar 2025 18:33:02 +0100 Subject: [PATCH 05/14] Apply suggestions from code review --- subworkflows/local/post_variantcalling/main.nf | 4 ---- 1 file changed, 4 deletions(-) diff --git a/subworkflows/local/post_variantcalling/main.nf b/subworkflows/local/post_variantcalling/main.nf index 0ad6c321c4..67ff98cea7 100644 --- a/subworkflows/local/post_variantcalling/main.nf +++ b/subworkflows/local/post_variantcalling/main.nf @@ -26,10 +26,6 @@ workflow POST_VARIANTCALLING { } if (normalize_vcfs) { - germline_vcfs.view { "germline:" + it } - tumor_only_vcfs.view { "tumor_only:" + it } - somatic_vcfs.view { "somatic:" + it } - NORMALIZE_VCFS(germline_vcfs, tumor_only_vcfs, somatic_vcfs, fasta) vcfs = vcfs.mix(NORMALIZE_VCFS.out.vcfs) From f9310a773cae147cbe445f67faab300cc16970c2 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 3 Mar 2025 18:34:24 +0100 Subject: [PATCH 06/14] sort modules import --- subworkflows/local/vcf_normalization/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/local/vcf_normalization/main.nf b/subworkflows/local/vcf_normalization/main.nf index a9ac190bbb..aaaafacd16 100644 --- a/subworkflows/local/vcf_normalization/main.nf +++ b/subworkflows/local/vcf_normalization/main.nf @@ -2,9 +2,9 @@ // Import modules include { ADD_INFO_TO_VCF } from '../../../modules/local/add_info_to_vcf' -include { TABIX_BGZIPTABIX as TABIX_EXT_VCF } from '../../../modules/nf-core/tabix/bgziptabix' include { BCFTOOLS_NORM as VCFS_NORM } from '../../../modules/nf-core/bcftools/norm' include { BCFTOOLS_SORT as VCFS_NORM_SORT } from '../../../modules/nf-core/bcftools/sort' +include { TABIX_BGZIPTABIX as TABIX_EXT_VCF } from '../../../modules/nf-core/tabix/bgziptabix' include { TABIX_TABIX as TABIX_VCFS_NORM_SORT } from '../../../modules/nf-core/tabix/tabix' // Workflow to normalize, compress, and index VCF files From a87b50b5c4d99ec677fdebf101aa7ed891a8573d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 3 Mar 2025 19:02:01 +0100 Subject: [PATCH 07/14] add file to .nftignore --- tests/.nftignore | 3 ++- tests/postprocess_concatenation.nf.test.snap | 14 +++----------- ...rocess_concatenation_normalization.nf.test.snap | 14 +++----------- tests/postprocess_normalization.nf.test.snap | 10 +--------- 4 files changed, 9 insertions(+), 32 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index edcf48378f..832d93f867 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,6 +1,7 @@ .DS_Store annotation/**/*.vcf.{gz,gz.tbi} csv/*.csv +multiqc/multiqc_data/bcftools*.txt multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt multiqc/multiqc_data/gatk-base-recalibrator-reported-empirical-plot.txt multiqc/multiqc_data/gatk_base_recalibrator.txt @@ -11,7 +12,7 @@ multiqc/multiqc_data/multiqc_picard_dups.txt multiqc/multiqc_data/multiqc_software_versions.txt multiqc/multiqc_data/multiqc_sources.txt multiqc/multiqc_data/picard_deduplication.txt -multiqc/multiqc_data/vcftools_tstv_by_qual.txt +multiqc/multiqc_data/vcftools*.txt multiqc/multiqc_plots/{svg,pdf,png}/*.{svg,pdf,png} multiqc/multiqc_report.html no_intervals.{bed,bed.gz,bed.gz.tbi} diff --git a/tests/postprocess_concatenation.nf.test.snap b/tests/postprocess_concatenation.nf.test.snap index 98924d1f50..deef980995 100644 --- a/tests/postprocess_concatenation.nf.test.snap +++ b/tests/postprocess_concatenation.nf.test.snap @@ -185,16 +185,8 @@ "variant_calling/haplotypecaller/testT/testT.haplotypecaller.vcf.gz.tbi" ], [ - "bcftools-stats-subtypes.txt:md5,698ccfbefaf3aa88da0ae8bceaf2bc87", - "bcftools_stats_indel-lengths.txt:md5,200444329f3f9392f299c61fbe9296b0", - "bcftools_stats_variant_depths.txt:md5,22cf631a39ef288c9e6c9facc68a61c6", - "bcftools_stats_vqc_Count_Indels.txt:md5,e372c4546a725d323f4a4350aa148ea0", - "bcftools_stats_vqc_Count_SNP.txt:md5,87e178164b6ed20014cd97d5590b64ab", - "bcftools_stats_vqc_Count_Transitions.txt:md5,20c63ab88b2e368bd958e6cdd1487855", - "bcftools_stats_vqc_Count_Transversions.txt:md5,754dfc24818b07f584fb0f205aaad50d", "multiqc_bcftools_stats.txt:md5,3769bb9010628ee799d088bfd9c60662", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", - "vcftools_tstv_by_count.txt:md5,c58d953b253b5ba4d65da093064e5fd5", "testN.freebayes.bcftools_stats.txt:md5,a4314ea6434629bae54b288f54f0c3bc", "testT.freebayes.bcftools_stats.txt:md5,62b05f3f02d3d3f92bd57f2f813feb7b", "testN.haplotypecaller.filtered.bcftools_stats.txt:md5,c6ae8e784f8d1550e0b49bb1cfe3128c", @@ -223,11 +215,11 @@ [ [ "testN.germline.vcf.gz", - "141a2cc53b0a9d4a0ab4d779cb1e487" + "184743db45c933febc5557d08b19f23c" ], [ "testT.germline.vcf.gz", - "9119ee2c970c37729dcb35d4b88f9d10" + "7bac441a7c84790f43d26a73e10be9b5" ], [ "testN.freebayes.vcf.gz", @@ -259,6 +251,6 @@ "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-03-03T18:24:54.468039835" + "timestamp": "2025-03-03T18:55:53.173733897" } } \ No newline at end of file diff --git a/tests/postprocess_concatenation_normalization.nf.test.snap b/tests/postprocess_concatenation_normalization.nf.test.snap index 6c0bf3a603..2088a46816 100644 --- a/tests/postprocess_concatenation_normalization.nf.test.snap +++ b/tests/postprocess_concatenation_normalization.nf.test.snap @@ -225,16 +225,8 @@ "variant_calling/normalized/testT/versions.yml" ], [ - "bcftools-stats-subtypes.txt:md5,bcf830fa75544b1ee9c84c8e68fe124c", - "bcftools_stats_indel-lengths.txt:md5,87f965fc8bc1f27539ce6577e79e5f36", - "bcftools_stats_variant_depths.txt:md5,8300a50a31f5ae71feaf1d8528507fb9", - "bcftools_stats_vqc_Count_Indels.txt:md5,0ef083b15189d878aed87681fc6a0422", - "bcftools_stats_vqc_Count_SNP.txt:md5,9a0e46eefc7ffa628381f0e8064f183e", - "bcftools_stats_vqc_Count_Transitions.txt:md5,e3c4a76d51aac2c8db625121c08ace11", - "bcftools_stats_vqc_Count_Transversions.txt:md5,37d9a00ecc45f57d7b8a4e9d6b0824cb", - "multiqc_bcftools_stats.txt:md5,44fb14c8a955205b78c585cc89e08846", + "multiqc_bcftools_stats.txt:md5,f89d57210865bd13c25956350add2112", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", - "vcftools_tstv_by_count.txt:md5,e8d339b0bf0292647bc4f24c8bd8a084", "testN.freebayes.norm.bcftools_stats.txt:md5,1cadbd27bb650441dadfd6984e44190f", "testN.germline.bcftools_stats.txt:md5,b8a3832c78fad6f4a182ea2a51fc82c3", "testT.freebayes.norm.bcftools_stats.txt:md5,2ea5c1d5a877254d4807cc6a82c23f43", @@ -277,7 +269,7 @@ [ [ "testN.germline.vcf.gz", - "184743db45c933febc5557d08b19f23c" + "141a2cc53b0a9d4a0ab4d779cb1e487" ], [ "testT.germline.vcf.gz", @@ -337,6 +329,6 @@ "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-03-03T18:26:55.378360589" + "timestamp": "2025-03-03T18:58:43.1136278" } } \ No newline at end of file diff --git a/tests/postprocess_normalization.nf.test.snap b/tests/postprocess_normalization.nf.test.snap index 83c7013e1f..bfffa99244 100644 --- a/tests/postprocess_normalization.nf.test.snap +++ b/tests/postprocess_normalization.nf.test.snap @@ -193,16 +193,8 @@ "variant_calling/normalized/testT/versions.yml" ], [ - "bcftools-stats-subtypes.txt:md5,14d79d00d95f319c28581b24d85b979b", - "bcftools_stats_indel-lengths.txt:md5,08d99ff43492e7225fd0afe8760b3e44", - "bcftools_stats_variant_depths.txt:md5,7e039ced7052f8c44f7fc8b8fc636f70", - "bcftools_stats_vqc_Count_Indels.txt:md5,d02630d8a8e1cb4759c207558be6e737", - "bcftools_stats_vqc_Count_SNP.txt:md5,c0ee5047463d19ece2bc64de139648d7", - "bcftools_stats_vqc_Count_Transitions.txt:md5,c11a77023dd62c9c4bd29a8139f02197", - "bcftools_stats_vqc_Count_Transversions.txt:md5,ae90d8ec6ad590d88c95edc82ea9884e", "multiqc_bcftools_stats.txt:md5,7cf61fb13b7221379888f0756d8f322e", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", - "vcftools_tstv_by_count.txt:md5,6c76fc304a7d346e999b584f73c19e8e", "testN.freebayes.norm.bcftools_stats.txt:md5,1cadbd27bb650441dadfd6984e44190f", "testT.freebayes.norm.bcftools_stats.txt:md5,2ea5c1d5a877254d4807cc6a82c23f43", "testN.haplotypecaller.norm.bcftools_stats.txt:md5,2d71e5e97bac8219bb6284d50d6b1e96", @@ -285,6 +277,6 @@ "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-03-03T18:28:42.107225989" + "timestamp": "2025-03-03T19:01:03.707942968" } } \ No newline at end of file From 236b23034d63b20b734683d8a96b95137fe7bd59 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 3 Mar 2025 20:13:52 +0100 Subject: [PATCH 08/14] regenerate snapshots --- tests/aligner-bwa-mem.nf.test.snap | 2 +- tests/aligner-bwa-mem2.nf.test.snap | 2 +- tests/aligner-dragmap.nf.test.snap | 2 +- tests/default.nf.test.snap | 8 +- tests/postprocess_concatenation.nf.test.snap | 4 +- ...s_concatenation_normalization.nf.test.snap | 6 +- tests/sentieon.nf.test.snap | 301 ------- tests/tumor-normal-pair.nf.test.snap | 375 +------- .../variant_calling_controlfreec.nf.test.snap | 410 +-------- tests/variant_calling_strelka.nf.test.snap | 833 +----------------- tests/variant_calling_strelka_bp.nf.test.snap | 470 +--------- 11 files changed, 94 insertions(+), 2319 deletions(-) diff --git a/tests/aligner-bwa-mem.nf.test.snap b/tests/aligner-bwa-mem.nf.test.snap index d9042b83df..80c1ee53f0 100644 --- a/tests/aligner-bwa-mem.nf.test.snap +++ b/tests/aligner-bwa-mem.nf.test.snap @@ -110,4 +110,4 @@ }, "timestamp": "2024-10-08T11:23:05.203586" } -} +} \ No newline at end of file diff --git a/tests/aligner-bwa-mem2.nf.test.snap b/tests/aligner-bwa-mem2.nf.test.snap index 1c4085e8bc..04b0bbe9e3 100644 --- a/tests/aligner-bwa-mem2.nf.test.snap +++ b/tests/aligner-bwa-mem2.nf.test.snap @@ -110,4 +110,4 @@ }, "timestamp": "2024-10-08T11:25:00.196657" } -} +} \ No newline at end of file diff --git a/tests/aligner-dragmap.nf.test.snap b/tests/aligner-dragmap.nf.test.snap index f1baf86444..fa01f8fc19 100644 --- a/tests/aligner-dragmap.nf.test.snap +++ b/tests/aligner-dragmap.nf.test.snap @@ -117,4 +117,4 @@ }, "timestamp": "2024-10-08T11:28:12.076906" } -} +} \ No newline at end of file diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 5ee15f72e8..30c1a16f0a 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -256,11 +256,6 @@ "variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi" ], [ - "bcftools_stats_indel-lengths.txt:md5,deccb75341ca46a6f09658f7fd9e348b", - "bcftools_stats_vqc_Count_Indels.txt:md5,7b2a64880b653ccf0400ed9073e290dd", - "bcftools_stats_vqc_Count_SNP.txt:md5,72e934e0e8ed9b9712105bbd66dd9ffd", - "bcftools_stats_vqc_Count_Transitions.txt:md5,72e934e0e8ed9b9712105bbd66dd9ffd", - "bcftools_stats_vqc_Count_Transversions.txt:md5,72e934e0e8ed9b9712105bbd66dd9ffd", "fastqc-status-check-heatmap.txt:md5,a020b9689ddeb4abec16b4854fe452f1", "fastqc_adapter_content_plot.txt:md5,2e1b72be741319e7fadbbb39d7e5b37d", "fastqc_per_base_n_content_plot.txt:md5,ad3b971a6bb4e8ba6c844c8a03584eb8", @@ -287,7 +282,6 @@ "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "samtools-stats-dp.txt:md5,c94f4d3ffa3f510552f90e173fdd9f9d", "samtools_alignment_plot.txt:md5,717f499a3543e7ee4c7a8454bf80aeca", - "vcftools_tstv_by_count.txt:md5,50efc5214fe2c39f21efb66a710d2ed6", "test.strelka.variants.bcftools_stats.txt:md5,86bd4938eed920d36f3f5937102a2967", "test.md.mosdepth.global.dist.txt:md5,b61e1acee11a6ddf7ce3232a5948a6a0", "test.md.mosdepth.region.dist.txt:md5,1a382f98d488d2ae3df83a0d87caafc1", @@ -329,6 +323,6 @@ "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-02-26T13:01:57.593464342" + "timestamp": "2025-03-03T19:41:34.274126011" } } \ No newline at end of file diff --git a/tests/postprocess_concatenation.nf.test.snap b/tests/postprocess_concatenation.nf.test.snap index deef980995..4e1f10d875 100644 --- a/tests/postprocess_concatenation.nf.test.snap +++ b/tests/postprocess_concatenation.nf.test.snap @@ -215,7 +215,7 @@ [ [ "testN.germline.vcf.gz", - "184743db45c933febc5557d08b19f23c" + "141a2cc53b0a9d4a0ab4d779cb1e487" ], [ "testT.germline.vcf.gz", @@ -251,6 +251,6 @@ "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-03-03T18:55:53.173733897" + "timestamp": "2025-03-03T19:43:34.799904548" } } \ No newline at end of file diff --git a/tests/postprocess_concatenation_normalization.nf.test.snap b/tests/postprocess_concatenation_normalization.nf.test.snap index 2088a46816..b7f5713b0d 100644 --- a/tests/postprocess_concatenation_normalization.nf.test.snap +++ b/tests/postprocess_concatenation_normalization.nf.test.snap @@ -225,7 +225,7 @@ "variant_calling/normalized/testT/versions.yml" ], [ - "multiqc_bcftools_stats.txt:md5,f89d57210865bd13c25956350add2112", + "multiqc_bcftools_stats.txt:md5,9f8b286d4679bf9920dcc9379752b480", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "testN.freebayes.norm.bcftools_stats.txt:md5,1cadbd27bb650441dadfd6984e44190f", "testN.germline.bcftools_stats.txt:md5,b8a3832c78fad6f4a182ea2a51fc82c3", @@ -273,7 +273,7 @@ ], [ "testT.germline.vcf.gz", - "9119ee2c970c37729dcb35d4b88f9d10" + "7bac441a7c84790f43d26a73e10be9b5" ], [ "testN.freebayes.vcf.gz", @@ -329,6 +329,6 @@ "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-03-03T18:58:43.1136278" + "timestamp": "2025-03-03T19:45:20.144893245" } } \ No newline at end of file diff --git a/tests/sentieon.nf.test.snap b/tests/sentieon.nf.test.snap index 5e89a3ae2b..e69de29bb2 100644 --- a/tests/sentieon.nf.test.snap +++ b/tests/sentieon.nf.test.snap @@ -1,301 +0,0 @@ -{ - "stub": { - "content": [ - 23, - { - "BCFTOOLS_STATS": { - "bcftools": 1.2 - }, - "FASTQC": { - "fastqc": "0.12.1" - }, - "GATK4_APPLYBQSR": { - "gatk4": "4.5.0.0" - }, - "GATK4_BASERECALIBRATOR": { - "gatk4": "4.5.0.0" - }, - "GATK4_MARKDUPLICATES": { - "gatk4": "4.5.0.0", - "samtools": "1.19.2" - }, - "INDEX_CRAM": { - "samtools": 1.21 - }, - "MOSDEPTH": { - "mosdepth": "0.3.8" - }, - "SAMTOOLS_STATS": { - "samtools": 1.21 - }, - "SENTIEON_BWAMEM": { - "sentieon": 202308.03, - "bwa": "0.7.17-r1188" - }, - "STRELKA_SINGLE": { - "strelka": "2.9.10" - }, - "VCFTOOLS_TSTV_COUNT": { - "vcftools": "0.1.16" - }, - "Workflow": { - "nf-core/sarek": "v3.6.0dev" - } - }, - [ - "csv", - "csv/markduplicates.csv", - "csv/markduplicates_no_table.csv", - "csv/recalibrated.csv", - "csv/variantcalled.csv", - "multiqc", - "multiqc/multiqc_data", - "multiqc/multiqc_plots", - "multiqc/multiqc_report.html", - "pipeline_info", - "pipeline_info/nf_core_sarek_software_mqc_versions.yml", - "preprocessing", - "preprocessing/markduplicates", - "preprocessing/markduplicates/test", - "preprocessing/markduplicates/test/test.cram", - "preprocessing/markduplicates/test/test.cram.crai", - "preprocessing/recal_table", - "preprocessing/recal_table/test", - "preprocessing/recal_table/test/test.recal.table", - "preprocessing/recalibrated", - "preprocessing/recalibrated/test", - "preprocessing/recalibrated/test/test.recal.cram", - "preprocessing/recalibrated/test/test.recal.cram.crai", - "reference", - "reports", - 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a/tests/postprocess_concatenation.nf.test +++ b/tests/postprocess_concatenation.nf.test @@ -24,7 +24,7 @@ nextflow_pipeline { // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') // vcf_files: All vcf files - def vcf_files = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz']) + def vcf_files = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz'], ignore: ['variant_calling/concat/testT/testT.germline.vcf.gz']) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/postprocess_concatenation.nf.test.snap b/tests/postprocess_concatenation.nf.test.snap index 4e1f10d875..ad84df90f3 100644 --- a/tests/postprocess_concatenation.nf.test.snap +++ b/tests/postprocess_concatenation.nf.test.snap @@ -215,11 +215,7 @@ [ [ "testN.germline.vcf.gz", - "141a2cc53b0a9d4a0ab4d779cb1e487" - ], - [ - "testT.germline.vcf.gz", - "7bac441a7c84790f43d26a73e10be9b5" + "184743db45c933febc5557d08b19f23c" ], [ "testN.freebayes.vcf.gz", @@ -251,6 +247,6 @@ "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-03-03T19:43:34.799904548" + "timestamp": "2025-03-04T09:37:59.21827169" } } \ No newline at end of file diff --git a/tests/postprocess_concatenation_normalization.nf.test b/tests/postprocess_concatenation_normalization.nf.test index 20f374e84d..33931e9a59 100644 --- a/tests/postprocess_concatenation_normalization.nf.test +++ b/tests/postprocess_concatenation_normalization.nf.test @@ -26,7 +26,7 @@ nextflow_pipeline { // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') // vcf_files: All vcf files - def vcf_files = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz']) + def vcf_files = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz'], ignore: ['variant_calling/concat/testT/testT.germline.vcf.gz']) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/postprocess_concatenation_normalization.nf.test.snap b/tests/postprocess_concatenation_normalization.nf.test.snap index b7f5713b0d..59d004e6f5 100644 --- a/tests/postprocess_concatenation_normalization.nf.test.snap +++ b/tests/postprocess_concatenation_normalization.nf.test.snap @@ -269,11 +269,7 @@ [ [ "testN.germline.vcf.gz", - "141a2cc53b0a9d4a0ab4d779cb1e487" - ], - [ - "testT.germline.vcf.gz", - "7bac441a7c84790f43d26a73e10be9b5" + "184743db45c933febc5557d08b19f23c" ], [ "testN.freebayes.vcf.gz", @@ -329,6 +325,6 @@ "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-03-03T19:45:20.144893245" + "timestamp": "2025-03-04T09:40:21.2962161" } } \ No newline at end of file From c05e3f287aa372cc2b3ac7a2dcfa1a2dfb358303 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 4 Mar 2025 10:12:04 +0100 Subject: [PATCH 11/14] fix snapshots --- tests/tumor-normal-pair.nf.test.snap | 369 ++++++++- .../variant_calling_controlfreec.nf.test.snap | 388 ++++++++- tests/variant_calling_strelka.nf.test.snap | 769 +++++++++++++++++- tests/variant_calling_strelka_bp.nf.test.snap | 450 +++++++++- 4 files changed, 1917 insertions(+), 59 deletions(-) diff --git a/tests/tumor-normal-pair.nf.test.snap b/tests/tumor-normal-pair.nf.test.snap index 4db06f306c..ea267fef6f 100644 --- a/tests/tumor-normal-pair.nf.test.snap +++ b/tests/tumor-normal-pair.nf.test.snap @@ -1,21 +1,230 @@ { "-profile test --input tests/csv/3.0/fastq_pair.csv": { "content": [ - 7, + 40, { + "BCFTOOLS_STATS": { + "bcftools": 1.2 + }, + "BWAMEM1_MEM": { + "bwa": "0.7.18-r1243-dirty", + "samtools": 1.2 + }, "FASTQC": { "fastqc": "0.12.1" }, + "GATK4_APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "GATK4_MARKDUPLICATES": { + "gatk4": "4.5.0.0", + "samtools": "1.19.2" + }, + "INDEX_CRAM": { + "samtools": 1.21 + }, + "MOSDEPTH": { + "mosdepth": "0.3.8" + }, + "SAMTOOLS_STATS": { + "samtools": 1.21 + }, + "STRELKA_SINGLE": { + "strelka": "2.9.10" + }, + "STRELKA_SOMATIC": { + "strelka": "2.9.10" + }, + "VCFTOOLS_TSTV_COUNT": { + "vcftools": "0.1.16" + }, "Workflow": { "nf-core/sarek": "v3.6.0dev" } }, [ "csv", + "csv/markduplicates.csv", + "csv/markduplicates_no_table.csv", + "csv/recalibrated.csv", + "csv/variantcalled.csv", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/bcftools_stats_indel-lengths.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Indels.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_SNP.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transitions.txt", + "multiqc/multiqc_data/bcftools_stats_vqc_Count_Transversions.txt", + "multiqc/multiqc_data/fastqc-status-check-heatmap.txt", + "multiqc/multiqc_data/fastqc_adapter_content_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_n_content_plot.txt", + "multiqc/multiqc_data/fastqc_per_base_sequence_quality_plot.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt", + "multiqc/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_counts_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/multiqc_data/fastqc_sequence_length_distribution_plot.txt", + "multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/multiqc_data/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt", + "multiqc/multiqc_data/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt", + "multiqc/multiqc_data/gatk-base-recalibrator-reported-empirical-plot.txt", + "multiqc/multiqc_data/gatk_base_recalibrator.txt", + "multiqc/multiqc_data/mosdepth-coverage-per-contig-single.txt", + "multiqc/multiqc_data/mosdepth-cumcoverage-dist-id.txt", + "multiqc/multiqc_data/mosdepth_cov_dist.txt", + "multiqc/multiqc_data/mosdepth_cumcov_dist.txt", + "multiqc/multiqc_data/mosdepth_perchrom.txt", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc_bcftools_stats.txt", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_fastqc.txt", + "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_picard_dups.txt", + "multiqc/multiqc_data/multiqc_samtools_stats.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_data/picard_deduplication.txt", + "multiqc/multiqc_data/picard_histogram.txt", + "multiqc/multiqc_data/picard_histogram_1.txt", + "multiqc/multiqc_data/picard_histogram_2.txt", + "multiqc/multiqc_data/samtools-stats-dp.txt", + "multiqc/multiqc_data/samtools_alignment_plot.txt", + "multiqc/multiqc_data/vcftools_tstv_by_count.txt", + "multiqc/multiqc_data/vcftools_tstv_by_qual.txt", + 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"multiqc/multiqc_plots/svg/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.svg", + "multiqc/multiqc_plots/svg/gatk-base-recalibrator-reported-empirical-plot.svg", + "multiqc/multiqc_plots/svg/general_stats_table.svg", + "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-single-cnt.svg", + "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-single-pct.svg", + "multiqc/multiqc_plots/svg/mosdepth-cumcoverage-dist-id.svg", + "multiqc/multiqc_plots/svg/picard_deduplication-cnt.svg", + "multiqc/multiqc_plots/svg/picard_deduplication-pct.svg", + "multiqc/multiqc_plots/svg/samtools-stats-dp.svg", + "multiqc/multiqc_plots/svg/samtools_alignment_plot-cnt.svg", + "multiqc/multiqc_plots/svg/samtools_alignment_plot-pct.svg", + "multiqc/multiqc_plots/svg/vcftools_tstv_by_count.svg", + "multiqc/multiqc_plots/svg/vcftools_tstv_by_qual.svg", + "multiqc/multiqc_report.html", "pipeline_info", "pipeline_info/nf_core_sarek_software_mqc_versions.yml", + "preprocessing", + "preprocessing/markduplicates", + "preprocessing/markduplicates/test", + "preprocessing/markduplicates/test/test.md.cram", + "preprocessing/markduplicates/test/test.md.cram.crai", + "preprocessing/markduplicates/test2", + "preprocessing/markduplicates/test2/test2.md.cram", + "preprocessing/markduplicates/test2/test2.md.cram.crai", + "preprocessing/recal_table", + "preprocessing/recal_table/test", + "preprocessing/recal_table/test/test.recal.table", + "preprocessing/recal_table/test2", + "preprocessing/recal_table/test2/test2.recal.table", + "preprocessing/recalibrated", + "preprocessing/recalibrated/test", + "preprocessing/recalibrated/test/test.recal.cram", + "preprocessing/recalibrated/test/test.recal.cram.crai", + "preprocessing/recalibrated/test2", + "preprocessing/recalibrated/test2/test2.recal.cram", + "preprocessing/recalibrated/test2/test2.recal.cram.crai", "reference", "reports", + "reports/bcftools", + "reports/bcftools/strelka", + "reports/bcftools/strelka/test", + "reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt", + "reports/bcftools/strelka/test2_vs_test", + "reports/bcftools/strelka/test2_vs_test/test2_vs_test.strelka.somatic_indels.bcftools_stats.txt", + "reports/bcftools/strelka/test2_vs_test/test2_vs_test.strelka.somatic_snvs.bcftools_stats.txt", "reports/fastqc", "reports/fastqc/test-test_L1", "reports/fastqc/test-test_L1/test-test_L1_1_fastqc.html", @@ -26,22 +235,170 @@ "reports/fastqc/test2-test_L1/test2-test_L1_1_fastqc.html", "reports/fastqc/test2-test_L1/test2-test_L1_1_fastqc.zip", "reports/fastqc/test2-test_L1/test2-test_L1_2_fastqc.html", - "reports/fastqc/test2-test_L1/test2-test_L1_2_fastqc.zip" + "reports/fastqc/test2-test_L1/test2-test_L1_2_fastqc.zip", + "reports/markduplicates", + "reports/markduplicates/test", + "reports/markduplicates/test/test.md.cram.metrics", + "reports/markduplicates/test2", + "reports/markduplicates/test2/test2.md.cram.metrics", + "reports/mosdepth", + "reports/mosdepth/test", + 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+ "sample4_vs_sample3.manta.somatic_sv.vcf.gz", + "d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "sample3.strelka.genome.vcf.gz", + "aac21bf1449d3c7361c14054b08f8ed1" + ], + [ + "sample3.strelka.variants.vcf.gz", + "dbea8798de92494c7a1fbf686c363696" + ], + [ + "sample4_vs_sample3.strelka.somatic_indels.vcf.gz", + "6b8a01b52186fcaf3ec74e5bf1b5426" + ], + [ + "sample4_vs_sample3.strelka.somatic_snvs.vcf.gz", + "866236c526138e4e08fdc2fa87b08417" + ] ] ], "meta": { "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-03-03T19:57:00.195979931" + "timestamp": "2025-03-04T10:06:09.203619973" } } \ No newline at end of file From 7f4fa7529b13e228df3cc011938ebfee5f420e63 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 4 Mar 2025 10:44:50 +0100 Subject: [PATCH 12/14] update snapshot --- tests/start_from_markduplicates.nf.test.snap | 228 +++++++++--------- ...art_from_preparerecalibration.nf.test.snap | 26 +- tests/start_from_recalibration.nf.test.snap | 106 ++++---- 3 files changed, 166 insertions(+), 194 deletions(-) diff --git a/tests/start_from_markduplicates.nf.test.snap b/tests/start_from_markduplicates.nf.test.snap index b9abf0923e..ea6ce47dea 100644 --- a/tests/start_from_markduplicates.nf.test.snap +++ b/tests/start_from_markduplicates.nf.test.snap @@ -1,7 +1,7 @@ { - "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools null": { + "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --tools null": { "content": [ - 9, + 13, { "GATK4_APPLYBQSR": { "gatk4": "4.5.0.0" @@ -9,6 +9,13 @@ "GATK4_BASERECALIBRATOR": { "gatk4": "4.5.0.0" }, + "GATK4_MARKDUPLICATES": { + "gatk4": "4.5.0.0", + "samtools": "1.19.2" + }, + "INDEX_CRAM": { + "samtools": 1.21 + }, "MOSDEPTH": { "mosdepth": "0.3.8" }, @@ -21,6 +28,9 @@ }, [ "csv", + "csv/markduplicates.csv", + "csv/markduplicates_no_table.csv", + "csv/recalibrated.csv", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt", @@ -36,9 +46,14 @@ "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_picard_dups.txt", "multiqc/multiqc_data/multiqc_samtools_stats.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_data/picard_deduplication.txt", + "multiqc/multiqc_data/picard_histogram.txt", + "multiqc/multiqc_data/picard_histogram_1.txt", + "multiqc/multiqc_data/picard_histogram_2.txt", "multiqc/multiqc_data/samtools-stats-dp.txt", "multiqc/multiqc_data/samtools_alignment_plot.txt", "multiqc/multiqc_plots", @@ -50,6 +65,8 @@ "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-single-cnt.pdf", "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-single-pct.pdf", "multiqc/multiqc_plots/pdf/mosdepth-cumcoverage-dist-id.pdf", + "multiqc/multiqc_plots/pdf/picard_deduplication-cnt.pdf", + "multiqc/multiqc_plots/pdf/picard_deduplication-pct.pdf", "multiqc/multiqc_plots/pdf/samtools-stats-dp.pdf", "multiqc/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf", "multiqc/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf", @@ -61,6 +78,8 @@ "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-single-cnt.png", "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-single-pct.png", "multiqc/multiqc_plots/png/mosdepth-cumcoverage-dist-id.png", + "multiqc/multiqc_plots/png/picard_deduplication-cnt.png", + "multiqc/multiqc_plots/png/picard_deduplication-pct.png", "multiqc/multiqc_plots/png/samtools-stats-dp.png", "multiqc/multiqc_plots/png/samtools_alignment_plot-cnt.png", "multiqc/multiqc_plots/png/samtools_alignment_plot-pct.png", @@ -72,6 +91,8 @@ "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-single-cnt.svg", "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-single-pct.svg", "multiqc/multiqc_plots/svg/mosdepth-cumcoverage-dist-id.svg", + "multiqc/multiqc_plots/svg/picard_deduplication-cnt.svg", + "multiqc/multiqc_plots/svg/picard_deduplication-pct.svg", "multiqc/multiqc_plots/svg/samtools-stats-dp.svg", "multiqc/multiqc_plots/svg/samtools_alignment_plot-cnt.svg", "multiqc/multiqc_plots/svg/samtools_alignment_plot-pct.svg", @@ -79,50 +100,85 @@ "pipeline_info", "pipeline_info/nf_core_sarek_software_mqc_versions.yml", "preprocessing", + "preprocessing/markduplicates", + "preprocessing/markduplicates/test", + "preprocessing/markduplicates/test/test.md.cram", + "preprocessing/markduplicates/test/test.md.cram.crai", "preprocessing/recal_table", "preprocessing/recal_table/test", "preprocessing/recal_table/test/test.recal.table", + "preprocessing/recalibrated", + "preprocessing/recalibrated/test", + "preprocessing/recalibrated/test/test.recal.cram", + "preprocessing/recalibrated/test/test.recal.cram.crai", "reference", "reports", + "reports/markduplicates", + "reports/markduplicates/test", + "reports/markduplicates/test/test.md.cram.metrics", "reports/mosdepth", "reports/mosdepth/test", - "reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt", - "reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt", - "reports/mosdepth/test/test.sorted.mosdepth.summary.txt", - "reports/mosdepth/test/test.sorted.regions.bed.gz", - "reports/mosdepth/test/test.sorted.regions.bed.gz.csi", + "reports/mosdepth/test/test.md.mosdepth.global.dist.txt", + "reports/mosdepth/test/test.md.mosdepth.region.dist.txt", + "reports/mosdepth/test/test.md.mosdepth.summary.txt", + "reports/mosdepth/test/test.md.regions.bed.gz", + "reports/mosdepth/test/test.md.regions.bed.gz.csi", + "reports/mosdepth/test/test.recal.mosdepth.global.dist.txt", + "reports/mosdepth/test/test.recal.mosdepth.region.dist.txt", + "reports/mosdepth/test/test.recal.mosdepth.summary.txt", + "reports/mosdepth/test/test.recal.regions.bed.gz", + "reports/mosdepth/test/test.recal.regions.bed.gz.csi", "reports/samtools", "reports/samtools/test", - "reports/samtools/test/test.sorted.cram.stats" + "reports/samtools/test/test.md.cram.stats", + "reports/samtools/test/test.recal.cram.stats" ], [ - "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,d2650a5bec510d798e347f36a4d00e2d", - "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,f2123f7ee3d060c1547efc6247a04e42", - "mosdepth-coverage-per-contig-single.txt:md5,8b48f3336b063dcb1e086928b28a2cc6", - "mosdepth-cumcoverage-dist-id.txt:md5,3148977f0c4684ba681ee298d677fe38", - "mosdepth_cov_dist.txt:md5,9a531d5a5c05e568a1aeb2e738ac23c4", - "mosdepth_cumcov_dist.txt:md5,9a531d5a5c05e568a1aeb2e738ac23c4", - "mosdepth_perchrom.txt:md5,8b48f3336b063dcb1e086928b28a2cc6", + "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,902745b5a1915e5c1a25267b11bebbe7", + "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,832ed176357d6a5b4e50c718f5e4a704", + "mosdepth-coverage-per-contig-single.txt:md5,76d816c3f71faf2009c8a6f88092a2f3", + "mosdepth-cumcoverage-dist-id.txt:md5,3af8f7d8ed7d1fdff6118e0098258192", + "mosdepth_cov_dist.txt:md5,4a2236db76d75e45012f6d7c180c90d6", + "mosdepth_cumcov_dist.txt:md5,4a2236db76d75e45012f6d7c180c90d6", + "mosdepth_perchrom.txt:md5,76d816c3f71faf2009c8a6f88092a2f3", "multiqc_citations.txt:md5,7d0b4b866fa577272c48a1f3ad72e75d", - "multiqc_samtools_stats.txt:md5,7f5f43de35c194be7f5980b62eacfab7", - "samtools-stats-dp.txt:md5,85c4ca7a3a6f2534d4d329937be49966", - "samtools_alignment_plot.txt:md5,301dda049c8aa2f848c98c81f584c315", - "test.sorted.mosdepth.global.dist.txt:md5,bdb8f185c35dd1eec7ce2f69bce57972", - "test.sorted.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2", - "test.sorted.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40", - "test.sorted.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e", - "test.sorted.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d", - "test.sorted.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac" + "multiqc_samtools_stats.txt:md5,de9451d4736a410d09de58828761ea87", + "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "samtools-stats-dp.txt:md5,2247da9fa269d826da3f33ba6fa66954", + "samtools_alignment_plot.txt:md5,22572fcd0791878ed37ae2f48213cee2", + "test.md.mosdepth.global.dist.txt:md5,8e875e20e3fb9cf288d68c1d223f6fd5", + "test.md.mosdepth.region.dist.txt:md5,75e1ce7e55af51f4985fa91654a5ea2d", + "test.md.mosdepth.summary.txt:md5,b23cf96942b2ada3f41172a9349a1175", + "test.md.regions.bed.gz:md5,74cd0c779c7b3228adcf3b177333886a", + "test.md.regions.bed.gz.csi:md5,080731cdedcd389e72135f048d6e2e00", + "test.recal.mosdepth.global.dist.txt:md5,8e875e20e3fb9cf288d68c1d223f6fd5", + "test.recal.mosdepth.region.dist.txt:md5,75e1ce7e55af51f4985fa91654a5ea2d", + "test.recal.mosdepth.summary.txt:md5,b23cf96942b2ada3f41172a9349a1175", + "test.recal.regions.bed.gz:md5,74cd0c779c7b3228adcf3b177333886a", + "test.recal.regions.bed.gz.csi:md5,080731cdedcd389e72135f048d6e2e00", + "test.md.cram.stats:md5,f181d98f08ad94c3926ac149a87d834b", + "test.recal.cram.stats:md5,18346c938c7b1bfaf9ac9413fdba90d8" ], - "No CRAM files" + [ + [ + "test.md.cram", + "2f11e4fe3390b8ad0a1852616fd1da04" + ], + [ + "test.recal.cram", + "463ac3b905fbf4ddf113a94dbfa8d69f" + ] + ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2025-02-25T11:06:19.105018276" + "timestamp": "2024-11-09T16:12:33.604156" }, - "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --tools null": { + "-profile test --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --tools null": { "content": [ 13, { @@ -299,7 +355,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-11-09T16:12:33.604156" + "timestamp": "2024-11-09T16:18:25.238396" }, "-profile test --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --tools null": { "content": [ @@ -449,9 +505,9 @@ }, "timestamp": "2024-11-09T16:23:55.741166" }, - "-profile test --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --tools null": { + "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools null": { "content": [ - 13, + 9, { "GATK4_APPLYBQSR": { "gatk4": "4.5.0.0" @@ -459,13 +515,6 @@ "GATK4_BASERECALIBRATOR": { "gatk4": "4.5.0.0" }, - "GATK4_MARKDUPLICATES": { - "gatk4": "4.5.0.0", - "samtools": "1.19.2" - }, - "INDEX_CRAM": { - "samtools": 1.21 - }, "MOSDEPTH": { "mosdepth": "0.3.8" }, @@ -478,9 +527,6 @@ }, [ "csv", - "csv/markduplicates.csv", - "csv/markduplicates_no_table.csv", - "csv/recalibrated.csv", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt", @@ -496,14 +542,9 @@ "multiqc/multiqc_data/multiqc_citations.txt", "multiqc/multiqc_data/multiqc_data.json", "multiqc/multiqc_data/multiqc_general_stats.txt", - "multiqc/multiqc_data/multiqc_picard_dups.txt", "multiqc/multiqc_data/multiqc_samtools_stats.txt", "multiqc/multiqc_data/multiqc_software_versions.txt", "multiqc/multiqc_data/multiqc_sources.txt", - "multiqc/multiqc_data/picard_deduplication.txt", - "multiqc/multiqc_data/picard_histogram.txt", - "multiqc/multiqc_data/picard_histogram_1.txt", - "multiqc/multiqc_data/picard_histogram_2.txt", "multiqc/multiqc_data/samtools-stats-dp.txt", "multiqc/multiqc_data/samtools_alignment_plot.txt", "multiqc/multiqc_plots", @@ -515,8 +556,6 @@ "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-single-cnt.pdf", "multiqc/multiqc_plots/pdf/mosdepth-coverage-per-contig-single-pct.pdf", "multiqc/multiqc_plots/pdf/mosdepth-cumcoverage-dist-id.pdf", - "multiqc/multiqc_plots/pdf/picard_deduplication-cnt.pdf", - "multiqc/multiqc_plots/pdf/picard_deduplication-pct.pdf", "multiqc/multiqc_plots/pdf/samtools-stats-dp.pdf", "multiqc/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf", "multiqc/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf", @@ -528,8 +567,6 @@ "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-single-cnt.png", "multiqc/multiqc_plots/png/mosdepth-coverage-per-contig-single-pct.png", "multiqc/multiqc_plots/png/mosdepth-cumcoverage-dist-id.png", - "multiqc/multiqc_plots/png/picard_deduplication-cnt.png", - "multiqc/multiqc_plots/png/picard_deduplication-pct.png", "multiqc/multiqc_plots/png/samtools-stats-dp.png", "multiqc/multiqc_plots/png/samtools_alignment_plot-cnt.png", "multiqc/multiqc_plots/png/samtools_alignment_plot-pct.png", @@ -541,8 +578,6 @@ "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-single-cnt.svg", "multiqc/multiqc_plots/svg/mosdepth-coverage-per-contig-single-pct.svg", "multiqc/multiqc_plots/svg/mosdepth-cumcoverage-dist-id.svg", - "multiqc/multiqc_plots/svg/picard_deduplication-cnt.svg", - "multiqc/multiqc_plots/svg/picard_deduplication-pct.svg", "multiqc/multiqc_plots/svg/samtools-stats-dp.svg", "multiqc/multiqc_plots/svg/samtools_alignment_plot-cnt.svg", "multiqc/multiqc_plots/svg/samtools_alignment_plot-pct.svg", @@ -550,82 +585,47 @@ "pipeline_info", "pipeline_info/nf_core_sarek_software_mqc_versions.yml", "preprocessing", - "preprocessing/markduplicates", - "preprocessing/markduplicates/test", - "preprocessing/markduplicates/test/test.md.cram", - "preprocessing/markduplicates/test/test.md.cram.crai", "preprocessing/recal_table", "preprocessing/recal_table/test", "preprocessing/recal_table/test/test.recal.table", - "preprocessing/recalibrated", - "preprocessing/recalibrated/test", - "preprocessing/recalibrated/test/test.recal.cram", - "preprocessing/recalibrated/test/test.recal.cram.crai", "reference", "reports", - "reports/markduplicates", - "reports/markduplicates/test", - "reports/markduplicates/test/test.md.cram.metrics", "reports/mosdepth", "reports/mosdepth/test", - "reports/mosdepth/test/test.md.mosdepth.global.dist.txt", - "reports/mosdepth/test/test.md.mosdepth.region.dist.txt", - "reports/mosdepth/test/test.md.mosdepth.summary.txt", - "reports/mosdepth/test/test.md.regions.bed.gz", - "reports/mosdepth/test/test.md.regions.bed.gz.csi", - "reports/mosdepth/test/test.recal.mosdepth.global.dist.txt", - "reports/mosdepth/test/test.recal.mosdepth.region.dist.txt", - "reports/mosdepth/test/test.recal.mosdepth.summary.txt", - "reports/mosdepth/test/test.recal.regions.bed.gz", - "reports/mosdepth/test/test.recal.regions.bed.gz.csi", + "reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt", + "reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt", + "reports/mosdepth/test/test.sorted.mosdepth.summary.txt", + "reports/mosdepth/test/test.sorted.regions.bed.gz", + "reports/mosdepth/test/test.sorted.regions.bed.gz.csi", "reports/samtools", "reports/samtools/test", - "reports/samtools/test/test.md.cram.stats", - "reports/samtools/test/test.recal.cram.stats" + "reports/samtools/test/test.sorted.cram.stats" ], [ - "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,902745b5a1915e5c1a25267b11bebbe7", - "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,832ed176357d6a5b4e50c718f5e4a704", - "mosdepth-coverage-per-contig-single.txt:md5,76d816c3f71faf2009c8a6f88092a2f3", - "mosdepth-cumcoverage-dist-id.txt:md5,3af8f7d8ed7d1fdff6118e0098258192", - "mosdepth_cov_dist.txt:md5,4a2236db76d75e45012f6d7c180c90d6", - "mosdepth_cumcov_dist.txt:md5,4a2236db76d75e45012f6d7c180c90d6", - "mosdepth_perchrom.txt:md5,76d816c3f71faf2009c8a6f88092a2f3", + "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,d2650a5bec510d798e347f36a4d00e2d", + "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,f2123f7ee3d060c1547efc6247a04e42", + "mosdepth-coverage-per-contig-single.txt:md5,8b48f3336b063dcb1e086928b28a2cc6", + "mosdepth-cumcoverage-dist-id.txt:md5,3148977f0c4684ba681ee298d677fe38", + "mosdepth_cov_dist.txt:md5,9a531d5a5c05e568a1aeb2e738ac23c4", + "mosdepth_cumcov_dist.txt:md5,9a531d5a5c05e568a1aeb2e738ac23c4", + "mosdepth_perchrom.txt:md5,8b48f3336b063dcb1e086928b28a2cc6", "multiqc_citations.txt:md5,7d0b4b866fa577272c48a1f3ad72e75d", - "multiqc_samtools_stats.txt:md5,de9451d4736a410d09de58828761ea87", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "samtools-stats-dp.txt:md5,2247da9fa269d826da3f33ba6fa66954", - "samtools_alignment_plot.txt:md5,22572fcd0791878ed37ae2f48213cee2", - "test.md.mosdepth.global.dist.txt:md5,8e875e20e3fb9cf288d68c1d223f6fd5", - "test.md.mosdepth.region.dist.txt:md5,75e1ce7e55af51f4985fa91654a5ea2d", - "test.md.mosdepth.summary.txt:md5,b23cf96942b2ada3f41172a9349a1175", - "test.md.regions.bed.gz:md5,74cd0c779c7b3228adcf3b177333886a", - "test.md.regions.bed.gz.csi:md5,080731cdedcd389e72135f048d6e2e00", - "test.recal.mosdepth.global.dist.txt:md5,8e875e20e3fb9cf288d68c1d223f6fd5", - "test.recal.mosdepth.region.dist.txt:md5,75e1ce7e55af51f4985fa91654a5ea2d", - "test.recal.mosdepth.summary.txt:md5,b23cf96942b2ada3f41172a9349a1175", - "test.recal.regions.bed.gz:md5,74cd0c779c7b3228adcf3b177333886a", - "test.recal.regions.bed.gz.csi:md5,080731cdedcd389e72135f048d6e2e00", - "test.md.cram.stats:md5,f181d98f08ad94c3926ac149a87d834b", - "test.recal.cram.stats:md5,18346c938c7b1bfaf9ac9413fdba90d8" + "multiqc_samtools_stats.txt:md5,7f5f43de35c194be7f5980b62eacfab7", + "samtools-stats-dp.txt:md5,85c4ca7a3a6f2534d4d329937be49966", + "samtools_alignment_plot.txt:md5,301dda049c8aa2f848c98c81f584c315", + "test.sorted.mosdepth.global.dist.txt:md5,bdb8f185c35dd1eec7ce2f69bce57972", + "test.sorted.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2", + "test.sorted.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40", + "test.sorted.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e", + "test.sorted.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d", + "test.sorted.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac" ], - [ - [ - "test.md.cram", - "2f11e4fe3390b8ad0a1852616fd1da04" - ], - [ - "test.recal.cram", - "463ac3b905fbf4ddf113a94dbfa8d69f" - ] - ] + "No CRAM files" ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nf-test": "0.9.2", + "nextflow": "24.10.4" }, - "timestamp": "2024-11-09T16:18:25.238396" + "timestamp": "2025-02-25T11:06:19.105018276" } } \ No newline at end of file diff --git a/tests/start_from_preparerecalibration.nf.test.snap b/tests/start_from_preparerecalibration.nf.test.snap index e029f9562b..57aaf225e3 100644 --- a/tests/start_from_preparerecalibration.nf.test.snap +++ b/tests/start_from_preparerecalibration.nf.test.snap @@ -62,7 +62,7 @@ }, "timestamp": "2025-02-25T11:13:54.836864751" }, - "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka": { + "-profile test --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka": { "content": [ 10, { @@ -157,15 +157,8 @@ "variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi" ], [ - "bcftools-stats-subtypes.txt:md5,08ac2a27511e23e15734fa84e97b53bb", - "bcftools_stats_indel-lengths.txt:md5,e2ae4bb4c56cff896db88a20ff2933d9", - "bcftools_stats_vqc_Count_Indels.txt:md5,aeeb155cb7bf39e5f349ce38dbe1699f", - "bcftools_stats_vqc_Count_SNP.txt:md5,ad63f8dfcc15fdc738b1e8ff54c8e452", - "bcftools_stats_vqc_Count_Transitions.txt:md5,6155d186233346cda2cb67147db8f6e7", - "bcftools_stats_vqc_Count_Transversions.txt:md5,60a0122e9d3828a4019336a87e158e42", "multiqc_bcftools_stats.txt:md5,3a9838b06c741231489075203469d2c4", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", - "vcftools_tstv_by_count.txt:md5,5ca47a28d7ae697981041d8b458ae889", "test.strelka.variants.bcftools_stats.txt:md5,3b37a441393a9329104451f44e56c619", "test.strelka.variants.FILTER.summary:md5,39ff2cc8eb7495a14a6b76e0ab627027", "test.strelka.variants.TsTv.count:md5,ee7dafc8d941b8502a04a63dc3126fff" @@ -184,11 +177,11 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-25T11:21:36.207625522" + "timestamp": "2025-03-04T10:36:30.587958704" }, - "-profile test --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka": { + "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka": { "content": [ 10, { @@ -283,15 +276,8 @@ "variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi" ], [ - "bcftools-stats-subtypes.txt:md5,08ac2a27511e23e15734fa84e97b53bb", - "bcftools_stats_indel-lengths.txt:md5,e2ae4bb4c56cff896db88a20ff2933d9", - "bcftools_stats_vqc_Count_Indels.txt:md5,aeeb155cb7bf39e5f349ce38dbe1699f", - "bcftools_stats_vqc_Count_SNP.txt:md5,ad63f8dfcc15fdc738b1e8ff54c8e452", - "bcftools_stats_vqc_Count_Transitions.txt:md5,6155d186233346cda2cb67147db8f6e7", - "bcftools_stats_vqc_Count_Transversions.txt:md5,60a0122e9d3828a4019336a87e158e42", "multiqc_bcftools_stats.txt:md5,3a9838b06c741231489075203469d2c4", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", - "vcftools_tstv_by_count.txt:md5,5ca47a28d7ae697981041d8b458ae889", "test.strelka.variants.bcftools_stats.txt:md5,3b37a441393a9329104451f44e56c619", "test.strelka.variants.FILTER.summary:md5,39ff2cc8eb7495a14a6b76e0ab627027", "test.strelka.variants.TsTv.count:md5,ee7dafc8d941b8502a04a63dc3126fff" @@ -310,9 +296,9 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-25T11:24:01.982167502" + "timestamp": "2025-03-04T10:34:32.128398501" }, "-profile test --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --tools null": { "content": [ diff --git a/tests/start_from_recalibration.nf.test.snap b/tests/start_from_recalibration.nf.test.snap index 3022af9caa..ae1be0ca4a 100644 --- a/tests/start_from_recalibration.nf.test.snap +++ b/tests/start_from_recalibration.nf.test.snap @@ -1,21 +1,17 @@ { - "-profile test --input tests/csv/3.0/mapped_single_cram.csv --step recalibrate --tools null": { + "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step recalibrate --tools null": { "content": [ - 9, + 6, { "GATK4_APPLYBQSR": { "gatk4": "4.5.0.0" }, - "INDEX_CRAM": { - "samtools": 1.21 - }, "Workflow": { "nf-core/sarek": "v3.6.0dev" } }, [ "csv", - "csv/recalibrated.csv", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -27,46 +23,22 @@ "pipeline_info", "pipeline_info/nf_core_sarek_software_mqc_versions.yml", "preprocessing", - "preprocessing/recalibrated", - "preprocessing/recalibrated/test", - "preprocessing/recalibrated/test/test.recal.cram", - "preprocessing/recalibrated/test/test.recal.cram.crai", - "reference", - "reports", - "reports/mosdepth", - "reports/mosdepth/test", - "reports/mosdepth/test/test.recal.mosdepth.global.dist.txt", - "reports/mosdepth/test/test.recal.mosdepth.region.dist.txt", - "reports/mosdepth/test/test.recal.mosdepth.summary.txt", - "reports/mosdepth/test/test.recal.regions.bed.gz", - "reports/mosdepth/test/test.recal.regions.bed.gz.csi", - "reports/samtools", - "reports/samtools/test", - "reports/samtools/test/test.recal.cram.stats" + "reference" ], [ - "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", - "test.recal.mosdepth.global.dist.txt:md5,bdb8f185c35dd1eec7ce2f69bce57972", - "test.recal.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2", - "test.recal.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40", - "test.recal.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e", - "test.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d", - "test.recal.cram.stats:md5,1aacf5ac46a0e600925934cf9ee92fc4" + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" ], [ - [ - "test.recal.cram", - "463ac3b905fbf4ddf113a94dbfa8d69f" - ] + ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-25T11:49:03.810929379" + "timestamp": "2025-02-25T10:28:52.529668484" }, - "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step recalibrate --skip_tools baserecalibrator --tools strelka": { + "-profile test --input tests/csv/3.0/mapped_single_cram.csv --step recalibrate --skip_tools baserecalibrator --tools strelka": { "content": [ 10, { @@ -161,15 +133,8 @@ "variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi" ], [ - "bcftools-stats-subtypes.txt:md5,08ac2a27511e23e15734fa84e97b53bb", - "bcftools_stats_indel-lengths.txt:md5,e2ae4bb4c56cff896db88a20ff2933d9", - "bcftools_stats_vqc_Count_Indels.txt:md5,aeeb155cb7bf39e5f349ce38dbe1699f", - "bcftools_stats_vqc_Count_SNP.txt:md5,ad63f8dfcc15fdc738b1e8ff54c8e452", - "bcftools_stats_vqc_Count_Transitions.txt:md5,6155d186233346cda2cb67147db8f6e7", - "bcftools_stats_vqc_Count_Transversions.txt:md5,60a0122e9d3828a4019336a87e158e42", "multiqc_bcftools_stats.txt:md5,3a9838b06c741231489075203469d2c4", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", - "vcftools_tstv_by_count.txt:md5,5ca47a28d7ae697981041d8b458ae889", "test.strelka.variants.bcftools_stats.txt:md5,3b37a441393a9329104451f44e56c619", "test.strelka.variants.FILTER.summary:md5,39ff2cc8eb7495a14a6b76e0ab627027", "test.strelka.variants.TsTv.count:md5,ee7dafc8d941b8502a04a63dc3126fff" @@ -188,11 +153,11 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-25T11:48:12.066290454" + "timestamp": "2025-03-04T10:40:26.865507047" }, - "-profile test --input tests/csv/3.0/mapped_single_cram.csv --step recalibrate --skip_tools baserecalibrator --tools strelka": { + "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step recalibrate --skip_tools baserecalibrator --tools strelka": { "content": [ 10, { @@ -287,15 +252,8 @@ "variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi" ], [ - "bcftools-stats-subtypes.txt:md5,08ac2a27511e23e15734fa84e97b53bb", - "bcftools_stats_indel-lengths.txt:md5,e2ae4bb4c56cff896db88a20ff2933d9", - "bcftools_stats_vqc_Count_Indels.txt:md5,aeeb155cb7bf39e5f349ce38dbe1699f", - "bcftools_stats_vqc_Count_SNP.txt:md5,ad63f8dfcc15fdc738b1e8ff54c8e452", - "bcftools_stats_vqc_Count_Transitions.txt:md5,6155d186233346cda2cb67147db8f6e7", - "bcftools_stats_vqc_Count_Transversions.txt:md5,60a0122e9d3828a4019336a87e158e42", "multiqc_bcftools_stats.txt:md5,3a9838b06c741231489075203469d2c4", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", - "vcftools_tstv_by_count.txt:md5,5ca47a28d7ae697981041d8b458ae889", "test.strelka.variants.bcftools_stats.txt:md5,3b37a441393a9329104451f44e56c619", "test.strelka.variants.FILTER.summary:md5,39ff2cc8eb7495a14a6b76e0ab627027", "test.strelka.variants.TsTv.count:md5,ee7dafc8d941b8502a04a63dc3126fff" @@ -314,23 +272,27 @@ ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.4" + "nextflow": "25.01.0" }, - "timestamp": "2025-02-25T11:49:59.953841611" + "timestamp": "2025-03-04T10:38:26.433544236" }, - "-profile test --input tests/csv/3.0/mapped_single_bam.csv --step recalibrate --tools null": { + "-profile test --input tests/csv/3.0/mapped_single_cram.csv --step recalibrate --tools null": { "content": [ - 6, + 9, { "GATK4_APPLYBQSR": { "gatk4": "4.5.0.0" }, + "INDEX_CRAM": { + "samtools": 1.21 + }, "Workflow": { "nf-core/sarek": "v3.6.0dev" } }, [ "csv", + "csv/recalibrated.csv", "multiqc", "multiqc/multiqc_data", "multiqc/multiqc_data/multiqc.log", @@ -342,19 +304,43 @@ "pipeline_info", "pipeline_info/nf_core_sarek_software_mqc_versions.yml", "preprocessing", - "reference" + "preprocessing/recalibrated", + "preprocessing/recalibrated/test", + "preprocessing/recalibrated/test/test.recal.cram", + "preprocessing/recalibrated/test/test.recal.cram.crai", + "reference", + "reports", + "reports/mosdepth", + "reports/mosdepth/test", + "reports/mosdepth/test/test.recal.mosdepth.global.dist.txt", + "reports/mosdepth/test/test.recal.mosdepth.region.dist.txt", + "reports/mosdepth/test/test.recal.mosdepth.summary.txt", + "reports/mosdepth/test/test.recal.regions.bed.gz", + "reports/mosdepth/test/test.recal.regions.bed.gz.csi", + "reports/samtools", + "reports/samtools/test", + "reports/samtools/test/test.recal.cram.stats" ], [ - "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f" + "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f", + "test.recal.mosdepth.global.dist.txt:md5,bdb8f185c35dd1eec7ce2f69bce57972", + "test.recal.mosdepth.region.dist.txt:md5,f1f1ad86fc280bced1888a5d7d25a3f2", + "test.recal.mosdepth.summary.txt:md5,32ea70ef1b99def3dc900b4afd513a40", + "test.recal.regions.bed.gz:md5,07bbc084a889f1cece4307fd00214a6e", + "test.recal.regions.bed.gz.csi:md5,c5d0be930ffc9e562f21519a0d488d5d", + "test.recal.cram.stats:md5,1aacf5ac46a0e600925934cf9ee92fc4" ], [ - + [ + "test.recal.cram", + "463ac3b905fbf4ddf113a94dbfa8d69f" + ] ] ], "meta": { "nf-test": "0.9.2", "nextflow": "24.10.4" }, - "timestamp": "2025-02-25T10:28:52.529668484" + "timestamp": "2025-02-25T11:49:03.810929379" } } \ No newline at end of file From 09aaed826c1fb20afcce9857ffddde6cdbf569bf Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 4 Mar 2025 10:45:35 +0100 Subject: [PATCH 13/14] not a stable file --- tests/postprocess_concatenation.nf.test | 2 +- tests/postprocess_concatenation.nf.test.snap | 6 +----- tests/postprocess_concatenation_normalization.nf.test | 2 +- .../postprocess_concatenation_normalization.nf.test.snap | 8 ++------ 4 files changed, 5 insertions(+), 13 deletions(-) diff --git a/tests/postprocess_concatenation.nf.test b/tests/postprocess_concatenation.nf.test index a39e9d2e40..7dd9aecac7 100644 --- a/tests/postprocess_concatenation.nf.test +++ b/tests/postprocess_concatenation.nf.test @@ -24,7 +24,7 @@ nextflow_pipeline { // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') // vcf_files: All vcf files - def vcf_files = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz'], ignore: ['variant_calling/concat/testT/testT.germline.vcf.gz']) + def vcf_files = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz'], ignore: ['variant_calling/concat/*/*.germline.vcf.gz']) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/postprocess_concatenation.nf.test.snap b/tests/postprocess_concatenation.nf.test.snap index ad84df90f3..c0988ebdd6 100644 --- a/tests/postprocess_concatenation.nf.test.snap +++ b/tests/postprocess_concatenation.nf.test.snap @@ -213,10 +213,6 @@ "testT.haplotypecaller.filtered.TsTv.count:md5,803d74e40f7716202bae2a3a81c1ddfc" ], [ - [ - "testN.germline.vcf.gz", - "184743db45c933febc5557d08b19f23c" - ], [ "testN.freebayes.vcf.gz", "1d98e39fe458af9020283de18c764055" @@ -247,6 +243,6 @@ "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-03-04T09:37:59.21827169" + "timestamp": "2025-03-04T10:42:43.935385919" } } \ No newline at end of file diff --git a/tests/postprocess_concatenation_normalization.nf.test b/tests/postprocess_concatenation_normalization.nf.test index 33931e9a59..a1195d6b40 100644 --- a/tests/postprocess_concatenation_normalization.nf.test +++ b/tests/postprocess_concatenation_normalization.nf.test @@ -26,7 +26,7 @@ nextflow_pipeline { // stable_path: All files in ${params.outdir}/ with stable content def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') // vcf_files: All vcf files - def vcf_files = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz'], ignore: ['variant_calling/concat/testT/testT.germline.vcf.gz']) + def vcf_files = getAllFilesFromDir(params.outdir, include: ['**/*.vcf.gz'], ignore: ['variant_calling/concat/*/*.germline.vcf.gz']) assertAll( { assert workflow.success}, { assert snapshot( diff --git a/tests/postprocess_concatenation_normalization.nf.test.snap b/tests/postprocess_concatenation_normalization.nf.test.snap index 59d004e6f5..9b49f366fc 100644 --- a/tests/postprocess_concatenation_normalization.nf.test.snap +++ b/tests/postprocess_concatenation_normalization.nf.test.snap @@ -225,7 +225,7 @@ "variant_calling/normalized/testT/versions.yml" ], [ - "multiqc_bcftools_stats.txt:md5,9f8b286d4679bf9920dcc9379752b480", + "multiqc_bcftools_stats.txt:md5,898ccdcc2b473e00692d3bc7ba5d9d30", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "testN.freebayes.norm.bcftools_stats.txt:md5,1cadbd27bb650441dadfd6984e44190f", "testN.germline.bcftools_stats.txt:md5,b8a3832c78fad6f4a182ea2a51fc82c3", @@ -267,10 +267,6 @@ "versions.yml:md5,7b0164f473a98fe0f8f097ae49c0e597" ], [ - [ - "testN.germline.vcf.gz", - "184743db45c933febc5557d08b19f23c" - ], [ "testN.freebayes.vcf.gz", "1d98e39fe458af9020283de18c764055" @@ -325,6 +321,6 @@ "nf-test": "0.9.2", "nextflow": "25.01.0" }, - "timestamp": "2025-03-04T09:40:21.2962161" + "timestamp": "2025-03-04T10:44:58.881133611" } } \ No newline at end of file From 4fb8dbb57b199ccbda6178accbe213021caede09 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Tue, 4 Mar 2025 11:05:29 +0100 Subject: [PATCH 14/14] add file to .nftignore --- tests/.nftignore | 1 + tests/default.nf.test.snap | 1 - tests/postprocess_concatenation.nf.test.snap | 1 - tests/postprocess_concatenation_normalization.nf.test.snap | 1 - tests/postprocess_normalization.nf.test.snap | 1 - tests/start_from_preparerecalibration.nf.test.snap | 2 -- tests/start_from_recalibration.nf.test.snap | 2 -- tests/tumor-normal-pair.nf.test.snap | 1 - tests/variant_calling_strelka.nf.test.snap | 5 ----- tests/variant_calling_strelka_bp.nf.test.snap | 2 -- 10 files changed, 1 insertion(+), 16 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index 832d93f867..3d5728ca53 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -6,6 +6,7 @@ multiqc/multiqc_data/fastqc_top_overrepresented_sequences_table.txt multiqc/multiqc_data/gatk-base-recalibrator-reported-empirical-plot.txt multiqc/multiqc_data/gatk_base_recalibrator.txt multiqc/multiqc_data/multiqc.log +multiqc/multiqc_data/multiqc_bcftools_stats.txt multiqc/multiqc_data/multiqc_data.json multiqc/multiqc_data/multiqc_general_stats.txt multiqc/multiqc_data/multiqc_picard_dups.txt diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 30c1a16f0a..dc47796d69 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -273,7 +273,6 @@ "mosdepth_cov_dist.txt:md5,8d0d7cb485a7bffb07da17b28f827120", "mosdepth_cumcov_dist.txt:md5,8d0d7cb485a7bffb07da17b28f827120", "mosdepth_perchrom.txt:md5,264db67a99d2c90ea7b075e33c201b77", - "multiqc_bcftools_stats.txt:md5,103ba59d44fc60e9308e64bbd0d0e504", "multiqc_citations.txt:md5,ace4ca89138a5f1e2be289c157c00bd9", "multiqc_fastqc.txt:md5,bde0d0bffa62228b33fb68b7e25b6ff8", "multiqc_samtools_stats.txt:md5,0f1e4c6c497d9a952765f9f3068ea4b9", diff --git a/tests/postprocess_concatenation.nf.test.snap b/tests/postprocess_concatenation.nf.test.snap index c0988ebdd6..663ddd170a 100644 --- a/tests/postprocess_concatenation.nf.test.snap +++ b/tests/postprocess_concatenation.nf.test.snap @@ -185,7 +185,6 @@ "variant_calling/haplotypecaller/testT/testT.haplotypecaller.vcf.gz.tbi" ], [ - "multiqc_bcftools_stats.txt:md5,3769bb9010628ee799d088bfd9c60662", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "testN.freebayes.bcftools_stats.txt:md5,a4314ea6434629bae54b288f54f0c3bc", "testT.freebayes.bcftools_stats.txt:md5,62b05f3f02d3d3f92bd57f2f813feb7b", diff --git a/tests/postprocess_concatenation_normalization.nf.test.snap b/tests/postprocess_concatenation_normalization.nf.test.snap index 9b49f366fc..2b446ca337 100644 --- a/tests/postprocess_concatenation_normalization.nf.test.snap +++ b/tests/postprocess_concatenation_normalization.nf.test.snap @@ -225,7 +225,6 @@ "variant_calling/normalized/testT/versions.yml" ], [ - "multiqc_bcftools_stats.txt:md5,898ccdcc2b473e00692d3bc7ba5d9d30", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "testN.freebayes.norm.bcftools_stats.txt:md5,1cadbd27bb650441dadfd6984e44190f", "testN.germline.bcftools_stats.txt:md5,b8a3832c78fad6f4a182ea2a51fc82c3", diff --git a/tests/postprocess_normalization.nf.test.snap b/tests/postprocess_normalization.nf.test.snap index bfffa99244..5a1f8a5ca1 100644 --- a/tests/postprocess_normalization.nf.test.snap +++ b/tests/postprocess_normalization.nf.test.snap @@ -193,7 +193,6 @@ "variant_calling/normalized/testT/versions.yml" ], [ - "multiqc_bcftools_stats.txt:md5,7cf61fb13b7221379888f0756d8f322e", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "testN.freebayes.norm.bcftools_stats.txt:md5,1cadbd27bb650441dadfd6984e44190f", "testT.freebayes.norm.bcftools_stats.txt:md5,2ea5c1d5a877254d4807cc6a82c23f43", diff --git a/tests/start_from_preparerecalibration.nf.test.snap b/tests/start_from_preparerecalibration.nf.test.snap index 57aaf225e3..b5c2398a2f 100644 --- a/tests/start_from_preparerecalibration.nf.test.snap +++ b/tests/start_from_preparerecalibration.nf.test.snap @@ -157,7 +157,6 @@ "variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi" ], [ - "multiqc_bcftools_stats.txt:md5,3a9838b06c741231489075203469d2c4", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "test.strelka.variants.bcftools_stats.txt:md5,3b37a441393a9329104451f44e56c619", "test.strelka.variants.FILTER.summary:md5,39ff2cc8eb7495a14a6b76e0ab627027", @@ -276,7 +275,6 @@ "variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi" ], [ - "multiqc_bcftools_stats.txt:md5,3a9838b06c741231489075203469d2c4", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "test.strelka.variants.bcftools_stats.txt:md5,3b37a441393a9329104451f44e56c619", "test.strelka.variants.FILTER.summary:md5,39ff2cc8eb7495a14a6b76e0ab627027", diff --git a/tests/start_from_recalibration.nf.test.snap b/tests/start_from_recalibration.nf.test.snap index ae1be0ca4a..b16e8576b0 100644 --- a/tests/start_from_recalibration.nf.test.snap +++ b/tests/start_from_recalibration.nf.test.snap @@ -133,7 +133,6 @@ "variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi" ], [ - "multiqc_bcftools_stats.txt:md5,3a9838b06c741231489075203469d2c4", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "test.strelka.variants.bcftools_stats.txt:md5,3b37a441393a9329104451f44e56c619", "test.strelka.variants.FILTER.summary:md5,39ff2cc8eb7495a14a6b76e0ab627027", @@ -252,7 +251,6 @@ "variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi" ], [ - "multiqc_bcftools_stats.txt:md5,3a9838b06c741231489075203469d2c4", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "test.strelka.variants.bcftools_stats.txt:md5,3b37a441393a9329104451f44e56c619", "test.strelka.variants.FILTER.summary:md5,39ff2cc8eb7495a14a6b76e0ab627027", diff --git a/tests/tumor-normal-pair.nf.test.snap b/tests/tumor-normal-pair.nf.test.snap index ea267fef6f..6dc9f024ff 100644 --- a/tests/tumor-normal-pair.nf.test.snap +++ b/tests/tumor-normal-pair.nf.test.snap @@ -315,7 +315,6 @@ "mosdepth_cov_dist.txt:md5,cb92686a4d6b7dcdeeee0ac13a63f369", "mosdepth_cumcov_dist.txt:md5,cb92686a4d6b7dcdeeee0ac13a63f369", "mosdepth_perchrom.txt:md5,e2bac78b61847b15c755dc7069670939", - "multiqc_bcftools_stats.txt:md5,7b8f1b48aa1c33067679168a3f0d9fd1", "multiqc_citations.txt:md5,ace4ca89138a5f1e2be289c157c00bd9", "multiqc_fastqc.txt:md5,2fd25e8c81f962594b801d5a9df3cd87", "multiqc_samtools_stats.txt:md5,60aa328e68503436f51e9a9b13dc6665", diff --git a/tests/variant_calling_strelka.nf.test.snap b/tests/variant_calling_strelka.nf.test.snap index 68fa18dbac..aa1ead5dca 100644 --- a/tests/variant_calling_strelka.nf.test.snap +++ b/tests/variant_calling_strelka.nf.test.snap @@ -134,7 +134,6 @@ "variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi" ], [ - "multiqc_bcftools_stats.txt:md5,c2674bda60d8fa805601c436afe16f18", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "sample3.strelka.variants.bcftools_stats.txt:md5,d505d381e8c3906788e4135bb975ff84", "sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt:md5,1c57e5cd6424157536276002ef1a58d6", @@ -288,7 +287,6 @@ "variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz.tbi" ], [ - "multiqc_bcftools_stats.txt:md5,cde557db5eb46f8325c06e9bb32e7a94", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "sample1.strelka.variants.bcftools_stats.txt:md5,2936f10f99295fb772d8c35f246e223d", "sample1.recal.mosdepth.global.dist.txt:md5,d9a4dd6429560b2b647da346050766c5", @@ -468,7 +466,6 @@ "variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi" ], [ - "multiqc_bcftools_stats.txt:md5,b2bbb90ef05598e1a70cf36be416c3e2", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "sample1.strelka.variants.bcftools_stats.txt:md5,2936f10f99295fb772d8c35f246e223d", "sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt:md5,1c57e5cd6424157536276002ef1a58d6", @@ -637,7 +634,6 @@ "variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz.tbi" ], [ - "multiqc_bcftools_stats.txt:md5,23c19e033f3086bec87c5e2022795e79", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "sample1.strelka.variants.bcftools_stats.txt:md5,0e829f5d31d768a8e99786786282c9ef", "sample1.recal.mosdepth.global.dist.txt:md5,d9a4dd6429560b2b647da346050766c5", @@ -804,7 +800,6 @@ "variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi" ], [ - "multiqc_bcftools_stats.txt:md5,e47ab6f334efa3a95dbd609a27711375", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "sample3.strelka.variants.bcftools_stats.txt:md5,c75a458b1aa0e1bae3b667d48684e13c", "sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt:md5,1c57e5cd6424157536276002ef1a58d6", diff --git a/tests/variant_calling_strelka_bp.nf.test.snap b/tests/variant_calling_strelka_bp.nf.test.snap index b17d34810e..dd443e9b2e 100644 --- a/tests/variant_calling_strelka_bp.nf.test.snap +++ b/tests/variant_calling_strelka_bp.nf.test.snap @@ -170,7 +170,6 @@ "variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi" ], [ - "multiqc_bcftools_stats.txt:md5,5c9c75a7ba51eec6d7ed539a5d0a2397", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "sample3.manta.diploid_sv.bcftools_stats.txt:md5,8adad91e1c8dc8db63cf9b3607bee3a0", "sample4_vs_sample3.manta.diploid_sv.bcftools_stats.txt:md5,17dc847445b98885bc18622f862f44d9", @@ -408,7 +407,6 @@ "variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi" ], [ - "multiqc_bcftools_stats.txt:md5,97bac5dbfe6cb21a78ca7f7327655b65", "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", "sample3.manta.diploid_sv.bcftools_stats.txt:md5,8adad91e1c8dc8db63cf9b3607bee3a0", "sample4_vs_sample3.manta.diploid_sv.bcftools_stats.txt:md5,17dc847445b98885bc18622f862f44d9",