diff --git a/.vscode/settings.json b/.vscode/settings.json new file mode 100644 index 0000000000..e810756abd --- /dev/null +++ b/.vscode/settings.json @@ -0,0 +1,3 @@ +{ + "nextflow.formatting.harshilAlignment": true +} diff --git a/CHANGELOG.md b/CHANGELOG.md index 845e69a462..df01931a20 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1664](https://github.com/nf-core/sarek/pull/1664) - Check if flowcell ID matches for read pair - [1663](https://github.com/nf-core/sarek/pull/1663) - Massive conda modules update - [1680](https://github.com/nf-core/sarek/pull/1682) - Add `bcftools_norm` in `POST_VARIANTCALLING` for normalization of all vcf files or for concatenated germline vcfs +- [1730](https://github.com/nf-core/sarek/pull/1730) - Enable Harshil Alignment™️ in VS Code workspace settings ### Changed @@ -29,9 +30,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1695](https://github.com/nf-core/sarek/pull/1695) - Update all modules - [1707](https://github.com/nf-core/sarek/pull/1707) - Un-hide parameters and clean up Json schema - [1708](https://github.com/nf-core/sarek/pull/1708) - Migrate pipeline pytest alignment and annotation tests to nf-test +- [1711](https://github.com/nf-core/sarek/pull/1711) - Migrate pipeline pytest strelka tests to nf-test ### Fixed +- [1624](https://github.com/nf-core/sarek/pull/1624) - Fix channel stalling for bcftools index - [1657](https://github.com/nf-core/sarek/pull/1657) - Update all actions used in the GHA CI - [1661](https://github.com/nf-core/sarek/pull/1661) - nf-test pipeline level tests - [1673](https://github.com/nf-core/sarek/pull/1673) - Print warning message instead of silent error with Nextflow versions prior to 24.08.0edge @@ -45,6 +48,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [1656](https://github.com/nf-core/sarek/pull/1656) - Retiring parameter `snpeff_genome` - [1709](https://github.com/nf-core/sarek/pull/1709) - Remove `Strelka` tumor-only somatic variant calling +- [1728](https://github.com/nf-core/sarek/pull/1728) - Remove BAM to CRAM conversion of input files for post-alignment entry points ### Dependencies @@ -108,7 +112,7 @@ Loametjåhkkå is another one of the main peaks of the Pårte massif. ### Added - [#1502](https://github.com/nf-core/sarek/pull/1502) - export CNVs into VCF format in `bam_variant_calling_cnvkit` -- [#1534](https://github.com/nf-core/sarek/pull/1534), [#1573](https://github.com/nf-core/sarek/pull/1573) - Handling `.fastq.gz.spring` files as input +- [#1534](https://github.com/nf-core/sarek/pull/1534), [#1573](https://github.com/nf-core/sarek/pull/1573), [#1734](https://github.com/nf-core/sarek/pull/1534) - Handling `.fastq.gz.spring` files as input - [#1593](https://github.com/nf-core/sarek/pull/1593) - Prepare release `3.4.2` ### Changed diff --git a/conf/test/markduplicates_bam.config b/conf/test/markduplicates_bam.config deleted file mode 100644 index 16060a2ba8..0000000000 --- a/conf/test/markduplicates_bam.config +++ /dev/null @@ -1,16 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple pipeline test. - - Use as follows: - nextflow run nf-core/sarek -profile test,, --outdir -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -params { - input = "${projectDir}/tests/csv/3.0/mapped_single_bam.csv" - step = 'markduplicates' - tools = null -} diff --git a/conf/test/markduplicates_cram.config b/conf/test/markduplicates_cram.config deleted file mode 100644 index e8f1d7c6f3..0000000000 --- a/conf/test/markduplicates_cram.config +++ /dev/null @@ -1,16 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple pipeline test. - - Use as follows: - nextflow run nf-core/sarek -profile test,, --outdir -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -params { - input = "${projectDir}/tests/csv/3.0/mapped_single_cram.csv" - step = 'markduplicates' - tools = null -} diff --git a/conf/test/prepare_recalibration_bam.config b/conf/test/prepare_recalibration_bam.config deleted file mode 100644 index 20a209b438..0000000000 --- a/conf/test/prepare_recalibration_bam.config +++ /dev/null @@ -1,16 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple pipeline test. - - Use as follows: - nextflow run nf-core/sarek -profile test,, --outdir -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -params { - input = "${projectDir}/tests/csv/3.0/mapped_single_bam.csv" - step = 'prepare_recalibration' - tools = null -} diff --git a/conf/test/prepare_recalibration_cram.config b/conf/test/prepare_recalibration_cram.config deleted file mode 100644 index ccab4977c9..0000000000 --- a/conf/test/prepare_recalibration_cram.config +++ /dev/null @@ -1,16 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for running minimal tests -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines input files and everything required to run a fast and simple pipeline test. - - Use as follows: - nextflow run nf-core/sarek -profile test,, --outdir -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -params { - input = "${projectDir}/tests/csv/3.0/mapped_single_cram.csv" - step = 'prepare_recalibration' - tools = null -} diff --git a/docs/images/sarek_subway.png b/docs/images/sarek_subway.png index f70415fbfe..f2f20ffc01 100644 Binary files a/docs/images/sarek_subway.png and b/docs/images/sarek_subway.png differ diff --git a/docs/images/sarek_subway.svg b/docs/images/sarek_subway.svg index d5129c4b36..62544b70fc 100644 --- a/docs/images/sarek_subway.svg +++ b/docs/images/sarek_subway.svg @@ -2,12 +2,12 @@ pre-processingcramspringfastqfastq/spring/ubamfastqfastq/spring/ubamGermline + y="846.21222" + id="tspan15">Germline •• deepvariant, deepvariant, freebayes + id="tspan18">freebayes GATK GATK haplotypecaller, + id="tspan21">haplotypecaller, mpileup, strelka2, + id="tspan23"> mpileup, strelka2, Sentieon haplotyper + id="tspan25"> Sentieon haplotyper • manta, tiddit + id="tspan27">• manta, tiddit • cnvkit• cnvkit [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools null ") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + input = "${projectDir}/tests/csv/3.0/mapped_single_bam.csv" + step = 'markduplicates' + skip_tools = "markduplicates" + tools = null + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + + test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --tools null ") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + input = "${projectDir}/tests/csv/3.0/mapped_single_cram.csv" + step = 'markduplicates' + tools = null + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step markduplicates --skip_tools markduplicates --tools null ") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + input = "${projectDir}/tests/csv/3.0/mapped_single_cram.csv" + step = 'markduplicates' + skip_tools = "markduplicates" + tools = null + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } +} diff --git a/tests/start_from_markduplicates.nf.test.snap b/tests/start_from_markduplicates.nf.test.snap new file mode 100644 index 0000000000..cf769bfcf4 --- /dev/null +++ b/tests/start_from_markduplicates.nf.test.snap @@ -0,0 +1,633 @@ +{ + "Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --skip_tools markduplicates --tools null ": { + "content": [ + 9, + { + "GATK4_APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "MOSDEPTH": { + "mosdepth": "0.3.8" + }, + "SAMTOOLS_STATS": { + "samtools": 1.21 + }, + "Workflow": { + "nf-core/sarek": "v3.5.0dev" + } + }, + [ + "csv", + "multiqc", + "multiqc/multiqc_data", + "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_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_general_stats.txt", + "multiqc/multiqc_data/multiqc_samtools_stats.txt", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_data/samtools-stats-dp.txt", + "multiqc/multiqc_data/samtools_alignment_plot.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.pdf", + "multiqc/multiqc_plots/pdf/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.pdf", + "multiqc/multiqc_plots/pdf/gatk-base-recalibrator-reported-empirical-plot.pdf", + "multiqc/multiqc_plots/pdf/general_stats_table.pdf", + "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/samtools-stats-dp.pdf", + "multiqc/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf", + "multiqc/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.png", + "multiqc/multiqc_plots/png/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.png", + "multiqc/multiqc_plots/png/gatk-base-recalibrator-reported-empirical-plot.png", + "multiqc/multiqc_plots/png/general_stats_table.png", + "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/samtools-stats-dp.png", + "multiqc/multiqc_plots/png/samtools_alignment_plot-cnt.png", + "multiqc/multiqc_plots/png/samtools_alignment_plot-pct.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.svg", + "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/samtools-stats-dp.svg", + "multiqc/multiqc_plots/svg/samtools_alignment_plot-cnt.svg", + "multiqc/multiqc_plots/svg/samtools_alignment_plot-pct.svg", + "multiqc/multiqc_report.html", + "pipeline_info", + "pipeline_info/nf_core_sarek_software_mqc_versions.yml", + "preprocessing", + "preprocessing/recal_table", + "preprocessing/recal_table/test", + "preprocessing/recal_table/test/test.recal.table", + "reference", + "reports", + "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/samtools", + "reports/samtools/test", + "reports/samtools/test/test.sorted.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", + "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" + ], + [ + + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-11-09T16:15:20.865586" + }, + "Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step markduplicates --tools null ": { + "content": [ + 13, + { + "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 + }, + "Workflow": { + "nf-core/sarek": "v3.5.0dev" + } + }, + [ + "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", + "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_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", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.pdf", + "multiqc/multiqc_plots/pdf/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.pdf", + "multiqc/multiqc_plots/pdf/gatk-base-recalibrator-reported-empirical-plot.pdf", + "multiqc/multiqc_plots/pdf/general_stats_table.pdf", + 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"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,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" + ], + [ + [ + "test.md.cram", + "2f11e4fe3390b8ad0a1852616fd1da04" + ], + [ + "test.recal.cram", + "463ac3b905fbf4ddf113a94dbfa8d69f" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-11-09T16:18:25.238396" + } +} \ No newline at end of file diff --git a/tests/start_from_preparerecalibration.nf.test b/tests/start_from_preparerecalibration.nf.test new file mode 100644 index 0000000000..8d445aaf40 --- /dev/null +++ b/tests/start_from_preparerecalibration.nf.test @@ -0,0 +1,162 @@ +nextflow_pipeline { + + name "Test pipeline when starting from prepare recalibration" + script "../main.nf" + tag "pipeline" + tag "pipeline_sarek" + + test("Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --tools null ") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + input = "${projectDir}/tests/csv/3.0/mapped_single_bam.csv" + step = 'prepare_recalibration' + tools = null + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka ") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + input = "${projectDir}/tests/csv/3.0/mapped_single_bam.csv" + step = 'prepare_recalibration' + skip_tools = "baserecalibrator" + tools = 'strelka' + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + + test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --tools null ") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + input = "${projectDir}/tests/csv/3.0/mapped_single_cram.csv" + step = 'prepare_recalibration' + tools = null + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka ") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + input = "${projectDir}/tests/csv/3.0/mapped_single_cram.csv" + step = 'prepare_recalibration' + skip_tools = "baserecalibrator" + tools = 'strelka' + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } +} diff --git a/tests/start_from_preparerecalibration.nf.test.snap b/tests/start_from_preparerecalibration.nf.test.snap new file mode 100644 index 0000000000..34bb44c643 --- /dev/null +++ b/tests/start_from_preparerecalibration.nf.test.snap @@ -0,0 +1,396 @@ +{ + "Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --tools null ": { + "content": [ + 7, + { + "GATK4_APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "Workflow": { + "nf-core/sarek": "v3.5.0dev" + } + }, + [ + "csv", + "csv/markduplicates.csv", + "multiqc", + "multiqc/multiqc_data", + "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/multiqc.log", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.pdf", + "multiqc/multiqc_plots/pdf/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.pdf", + "multiqc/multiqc_plots/pdf/gatk-base-recalibrator-reported-empirical-plot.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.png", + "multiqc/multiqc_plots/png/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.png", + "multiqc/multiqc_plots/png/gatk-base-recalibrator-reported-empirical-plot.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.svg", + "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_report.html", + "pipeline_info", + "pipeline_info/nf_core_sarek_software_mqc_versions.yml", + "preprocessing", + "preprocessing/recal_table", + "preprocessing/recal_table/test", + "preprocessing/recal_table/test/test.recal.table", + "reference" + ], + [ + "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,d2650a5bec510d798e347f36a4d00e2d", + "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,f2123f7ee3d060c1547efc6247a04e42", + "multiqc_citations.txt:md5,3815a9f79e41890653a0e0d602c92ac9" + ], + [ + + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-11-09T16:57:10.392231" + }, + "Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step prepare_recalibration --skip_tools baserecalibrator --tools strelka ": { + "content": [ + 10, + { + "BCFTOOLS_STATS": { + "bcftools": 1.2 + }, + "STRELKA_SINGLE": { + "strelka": "2.9.10" + }, + "VCFTOOLS_TSTV_COUNT": { + "vcftools": "0.1.16" + }, + "Workflow": { + "nf-core/sarek": "v3.5.0dev" + } + }, + [ + "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_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_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_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_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/strelka", + "reports/bcftools/strelka/test", + "reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt", + "reports/vcftools", + "reports/vcftools/strelka", + "reports/vcftools/strelka/test", + "reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary", + "reports/vcftools/strelka/test/test.strelka.variants.TsTv.count", + "reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual", + "variant_calling", + "variant_calling/strelka", + "variant_calling/strelka/test", + "variant_calling/strelka/test/test.strelka.genome.vcf.gz", + "variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi", + "variant_calling/strelka/test/test.strelka.variants.vcf.gz", + "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", + 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"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_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_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_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/strelka", + "reports/bcftools/strelka/test", + "reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt", + "reports/vcftools", + "reports/vcftools/strelka", + "reports/vcftools/strelka/test", + "reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary", + "reports/vcftools/strelka/test/test.strelka.variants.TsTv.count", + "reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual", + "variant_calling", + "variant_calling/strelka", + "variant_calling/strelka/test", + "variant_calling/strelka/test/test.strelka.genome.vcf.gz", + "variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi", + "variant_calling/strelka/test/test.strelka.variants.vcf.gz", + "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" + ], + [ + + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-11-09T17:02:51.883814" + }, + "Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step prepare_recalibration --tools null ": { + "content": [ + 10, + { + "GATK4_APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "GATK4_BASERECALIBRATOR": { + "gatk4": "4.5.0.0" + }, + "INDEX_CRAM": { + "samtools": 1.21 + }, + "Workflow": { + "nf-core/sarek": "v3.5.0dev" + } + }, + [ + "csv", + "csv/markduplicates.csv", + "csv/recalibrated.csv", + "multiqc", + "multiqc/multiqc_data", + "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/multiqc.log", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_plots", + "multiqc/multiqc_plots/pdf", + "multiqc/multiqc_plots/pdf/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.pdf", + "multiqc/multiqc_plots/pdf/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.pdf", + "multiqc/multiqc_plots/pdf/gatk-base-recalibrator-reported-empirical-plot.pdf", + "multiqc/multiqc_plots/png", + "multiqc/multiqc_plots/png/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.png", + "multiqc/multiqc_plots/png/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.png", + "multiqc/multiqc_plots/png/gatk-base-recalibrator-reported-empirical-plot.png", + "multiqc/multiqc_plots/svg", + "multiqc/multiqc_plots/svg/gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.svg", + "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_report.html", + "pipeline_info", + "pipeline_info/nf_core_sarek_software_mqc_versions.yml", + "preprocessing", + "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/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" + ], + [ + "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Count.txt:md5,d2650a5bec510d798e347f36a4d00e2d", + "gatk-base-recalibrator-quality-scores-plot_Pre-recalibration_Percent.txt:md5,f2123f7ee3d060c1547efc6247a04e42", + "multiqc_citations.txt:md5,3815a9f79e41890653a0e0d602c92ac9", + "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:md5,9f75ec16d22ce12c348cbd7477c9886e" + ], + [ + [ + "test.recal.cram", + "463ac3b905fbf4ddf113a94dbfa8d69f" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-11-09T17:01:30.130705" + } +} \ No newline at end of file diff --git a/tests/start_from_recalibration.nf.test b/tests/start_from_recalibration.nf.test new file mode 100644 index 0000000000..3549bd793a --- /dev/null +++ b/tests/start_from_recalibration.nf.test @@ -0,0 +1,162 @@ +nextflow_pipeline { + + name "Test pipeline when starting from recalibration" + script "../main.nf" + tag "pipeline" + tag "pipeline_sarek" + + test("Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step recalibrate --tools null ") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + input = "${projectDir}/tests/csv/3.0/prepare_recalibration_single_bam.csv" + step = 'recalibrate' + tools = null + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Run with profile test | --input tests/csv/3.0/mapped_single_bam.csv --step recalibrate --skip_tools baserecalibrator --tools strelka ") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + input = "${projectDir}/tests/csv/3.0/prepare_recalibration_single_bam.csv" + step = 'recalibrate' + skip_tools = "baserecalibrator" + tools = 'strelka' + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + + test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step recalibrate --tools null ") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + input = "${projectDir}/tests/csv/3.0/prepare_recalibration_single_cram.csv" + step = 'recalibrate' + tools = null + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step recalibrate --skip_tools baserecalibrator --tools strelka ") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + outdir = "$outputDir" + input = "${projectDir}/tests/csv/3.0/prepare_recalibration_single_cram.csv" + step = 'recalibrate' + skip_tools = "baserecalibrator" + tools = 'strelka' + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } +} diff --git a/tests/start_from_recalibration.nf.test.snap b/tests/start_from_recalibration.nf.test.snap new file mode 100644 index 0000000000..88a9995819 --- /dev/null +++ b/tests/start_from_recalibration.nf.test.snap @@ -0,0 +1,344 @@ +{ + "Run with profile test | --input tests/csv/3.0/mapped_single_cram.csv --step recalibrate --tools null ": { + "content": [ + 9, + { + "GATK4_APPLYBQSR": { + "gatk4": "4.5.0.0" + }, + "INDEX_CRAM": { + "samtools": 1.21 + }, + "Workflow": { + "nf-core/sarek": "v3.5.0dev" + } + }, + [ + "csv", + "csv/recalibrated.csv", + "multiqc", + "multiqc/multiqc_data", + "multiqc/multiqc_data/multiqc.log", + "multiqc/multiqc_data/multiqc_citations.txt", + "multiqc/multiqc_data/multiqc_data.json", + "multiqc/multiqc_data/multiqc_software_versions.txt", + "multiqc/multiqc_data/multiqc_sources.txt", + "multiqc/multiqc_report.html", + "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" + ], + [ + "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": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-11-09T17:22:03.443847" + }, + "Run with profile test | --input 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nextflow run main.nf -profile test,markduplicates_bam --outdir results - tags: - - input_bam - - gatk4/markduplicates - - preprocessing - files: - - path: results/csv/markduplicates.csv - md5sum: 8e9408ef8d4f9e6e00e531268eebd42a - - path: results/csv/markduplicates_no_table.csv - md5sum: f8b1b25fec472453a98c3f7f0e3a7953 - - path: results/csv/recalibrated.csv - md5sum: 1888a924bc70bd80165a96ad641e22d6 - - path: results/multiqc - - path: results/preprocessing/markduplicates/test/test.md.cram - # binary changes md5sums on reruns - - path: results/preprocessing/markduplicates/test/test.md.cram.crai - # binary changes md5sums on reruns - - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf - - path: results/preprocessing/recalibrated/test/test.recal.cram - # binary changes md5sums on reruns - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - # binary changes md5sums on reruns - - path: results/reports/markduplicates/test/test.md.cram.metrics - contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986 1178 1178", "100.0 1.911145 0 0"] - - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - - path: results/reports/mosdepth/test/test.md.regions.bed.gz - - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - - path: results/reports/samtools/test/test.md.cram.stats - # conda changes md5sums for test - - path: results/reports/samtools/test/test.recal.cram.stats - # conda changes md5sums for test - -- name: Run skip markduplicates bam from step markduplicates - command: nextflow run main.nf -profile test,markduplicates_bam,skip_markduplicates --outdir results - tags: - - input_bam - - markduplicates - - preprocessing - - skip_markduplicates - files: - - path: results/csv/recalibrated.csv - md5sum: 1888a924bc70bd80165a96ad641e22d6 - - path: results/multiqc - - path: results/preprocessing/converted/test/test.converted.cram - # binary changes md5sums on reruns - - path: results/preprocessing/converted/test/test.converted.cram.crai - # binary changes md5sums on reruns - - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 35d89a3811aa31711fc9815b6b80e6ec - - path: results/preprocessing/recalibrated/test/test.recal.cram - # binary changes md5sums on reruns - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - # binary changes md5sums on reruns - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - - path: results/reports/samtools/test/test.recal.cram.stats - # conda changes md5sums for test - - path: results/reports/samtools/test/test.sorted.cram.stats - # conda changes md5sums for test - - path: results/csv/markduplicates.csv - should_exist: false - - path: results/csv/markduplicates_no_table.csv - should_exist: false - - path: results/preprocessing/mapped/test/test.bam - should_exist: false - - path: results/preprocessing/mapped/test/test.sorted.bam - should_exist: false diff --git a/tests/test_markduplicates_from_cram.yml b/tests/test_markduplicates_from_cram.yml deleted file mode 100644 index ff28636112..0000000000 --- a/tests/test_markduplicates_from_cram.yml +++ /dev/null @@ -1,81 +0,0 @@ -- name: Run markduplicates starting from CRAM - command: nextflow run main.nf -profile test,markduplicates_cram --outdir results - tags: - - input_cram - - gatk4/markduplicates - - preprocessing - files: - - path: results/csv/markduplicates.csv - md5sum: 8e9408ef8d4f9e6e00e531268eebd42a - - path: results/csv/markduplicates_no_table.csv - md5sum: f8b1b25fec472453a98c3f7f0e3a7953 - - path: results/csv/recalibrated.csv - md5sum: 1888a924bc70bd80165a96ad641e22d6 - - path: results/multiqc - - path: results/preprocessing/markduplicates/test/test.md.cram - # binary changes md5sums on reruns - - path: results/preprocessing/markduplicates/test/test.md.cram.crai - # binary changes md5sums on reruns - - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf - - path: results/preprocessing/recalibrated/test/test.recal.cram - # binary changes md5sums on reruns - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - # binary changes md5sums on reruns - - path: results/reports/markduplicates/test/test.md.cram.metrics - contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986 1178 1178", "100.0 1.911145 0 0"] - - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - - path: results/reports/mosdepth/test/test.md.regions.bed.gz - - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - - path: results/reports/samtools/test/test.md.cram.stats - # conda changes md5sums for test - - path: results/reports/samtools/test/test.recal.cram.stats - # conda changes md5sums for test - - path: results/preprocessing/mapped/ - should_exist: false -- name: Run skip markduplicates cram from step markduplicates - command: nextflow run main.nf -profile test,markduplicates_cram,skip_markduplicates --outdir results - tags: - - input_cram - - markduplicates - - preprocessing - - skip_markduplicates - files: - - path: results/csv/recalibrated.csv - md5sum: 1888a924bc70bd80165a96ad641e22d6 - - path: results/multiqc - - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 35d89a3811aa31711fc9815b6b80e6ec - - path: results/preprocessing/recalibrated/test/test.recal.cram - # binary changes md5sums on reruns - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - # binary changes md5sums on reruns - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - - path: results/reports/samtools/test/test.recal.cram.stats - # conda changes md5sums for test - - path: results/reports/samtools/test/test.sorted.cram.stats - # conda changes md5sums for test - - path: results/csv/markduplicates.csv - should_exist: false - - path: results/csv/markduplicates_no_table.csv - should_exist: false - - path: results/preprocessing/mapped/test/test.sorted.cram - should_exist: false - - path: results/preprocessing/mapped/test/test.sorted.cram.crai - should_exist: false diff --git a/tests/test_prepare_recalibration_from_bam.yml b/tests/test_prepare_recalibration_from_bam.yml deleted file mode 100644 index 335a67deed..0000000000 --- a/tests/test_prepare_recalibration_from_bam.yml +++ /dev/null @@ -1,79 +0,0 @@ -- name: Run prepare_recalibration starting from bam - command: nextflow run main.nf -profile test,prepare_recalibration_bam --outdir results - tags: - - input_bam - - prepare_recalibration - - preprocessing - files: - - path: results/csv/markduplicates.csv - md5sum: 90e2ab85d8af642d6548af448a9d4226 - - path: results/csv/recalibrated.csv - md5sum: 1888a924bc70bd80165a96ad641e22d6 - - path: results/multiqc - - path: results/preprocessing/converted/test/test.converted.cram - # binary changes md5sums on reruns - - path: results/preprocessing/converted/test/test.converted.cram.crai - # binary changes md5sums on reruns - - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 35d89a3811aa31711fc9815b6b80e6ec - - path: results/preprocessing/recalibrated/test/test.recal.cram - # binary changes md5sums on reruns - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - # binary changes md5sums on reruns - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - - path: results/reports/samtools/test/test.recal.cram.stats - # conda changes md5sums for test - - path: results/preprocessing/mapped/ - should_exist: false - - path: results/preprocessing/markduplicates/ - should_exist: false -- name: Run prepare_recalibration starting from bam and skip baserecalibration - command: nextflow run main.nf -profile test,prepare_recalibration_bam,skip_bqsr --tools strelka --outdir results - tags: - - input_bam - - prepare_recalibration - - preprocessing - files: - - path: results/csv/variantcalled.csv - md5sum: 4d0effd3d8dc2b814230a189e7ca9dba - - path: results/multiqc - - path: results/preprocessing/converted/test/test.converted.cram - # binary changes md5sums on reruns - - path: results/preprocessing/converted/test/test.converted.cram.crai - # binary changes md5sums on reruns - - path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary - md5sum: 39ff2cc8eb7495a14a6b76e0ab627027 - - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count - md5sum: ee7dafc8d941b8502a04a63dc3126fff - - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual - # conda changes md5sums for test - - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/csv/recalibrated.csv - should_exist: false - - path: results/preprocessing/recal_table/test/test.recal.table - should_exist: false - - path: results/preprocessing/recalibrated/test/test.recal.cram - should_exist: false - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - should_exist: false - - path: results/reports/mosdepth - should_exist: false - - path: results/reports/samtools_stats - should_exist: false - - path: results/preprocessing/mapped/ - should_exist: false - - path: results/preprocessing/markduplicates/ - should_exist: false diff --git a/tests/test_prepare_recalibration_from_cram.yml b/tests/test_prepare_recalibration_from_cram.yml deleted file mode 100644 index 6e362ccd7b..0000000000 --- a/tests/test_prepare_recalibration_from_cram.yml +++ /dev/null @@ -1,79 +0,0 @@ -- name: Run prepare_recalibration starting from cram - command: nextflow run main.nf -profile test,prepare_recalibration_cram --outdir results - tags: - - input_cram - - prepare_recalibration - - preprocessing - files: - - path: results/csv/recalibrated.csv - md5sum: 1888a924bc70bd80165a96ad641e22d6 - - path: results/multiqc - - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 35d89a3811aa31711fc9815b6b80e6ec - - path: results/preprocessing/recalibrated/test/test.recal.cram - # binary changes md5sums on reruns - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - # binary changes md5sums on reruns - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - - path: results/reports/samtools/test/test.recal.cram.stats - # conda changes md5sums for test - - path: results/preprocessing/mapped/ - should_exist: false - - path: results/preprocessing/markduplicates/ - should_exist: false -- name: Run prepare_recalibration starting from cram and skip baserecalibration - command: nextflow run main.nf -profile test,prepare_recalibration_cram,skip_bqsr --tools strelka --outdir results - tags: - - input_cram - - prepare_recalibration - - preprocessing - files: - - path: results/csv/variantcalled.csv - md5sum: 4d0effd3d8dc2b814230a189e7ca9dba - - path: results/multiqc - - path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary - md5sum: 39ff2cc8eb7495a14a6b76e0ab627027 - - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count - md5sum: ee7dafc8d941b8502a04a63dc3126fff - - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual - # conda changes md5sums for test - - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/csv/recalibrated.csv - should_exist: false - - path: results/preprocessing/markduplicates/test/test.md.cram - should_exist: false - - path: results/preprocessing/markduplicates/test/test.md.cram.crai - should_exist: false - - path: results/preprocessing/recal_table/test/test.recal.table - should_exist: false - - path: results/preprocessing/recalibrated/test/test.recal.cram - should_exist: false - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - should_exist: false - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - should_exist: false - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - should_exist: false - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - should_exist: false - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - should_exist: false - - path: results/reports/samtools/test/test.recal.cram.stats - should_exist: false - - path: results/preprocessing/mapped/ - should_exist: false - - path: results/preprocessing/markduplicates/ - should_exist: false diff --git a/tests/test_recalibrate_from_bam.yml b/tests/test_recalibrate_from_bam.yml deleted file mode 100644 index fb96a3d305..0000000000 --- a/tests/test_recalibrate_from_bam.yml +++ /dev/null @@ -1,82 +0,0 @@ -- name: Run Recalibration starting from bam - command: nextflow run main.nf -profile test,recalibrate_bam --outdir results - tags: - - input_bam - - recalibrate - - preprocessing - files: - - path: results/csv/recalibrated.csv - md5sum: 1888a924bc70bd80165a96ad641e22d6 - - path: results/multiqc - - path: results/preprocessing/converted/test/test.converted.cram - # binary changes md5sums on reruns - - path: results/preprocessing/converted/test/test.converted.cram.crai - # binary changes md5sums on reruns - - path: results/preprocessing/recalibrated/test/test.recal.cram - # binary changes md5sums on reruns - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - # binary changes md5sums on reruns - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - - path: results/reports/samtools/test/test.recal.cram.stats - # conda changes md5sums for test - - path: results/preprocessing/mapped/ - should_exist: false - - path: results/preprocessing/markduplicates/ - should_exist: false -- name: Run Recalibration starting from bam and skip baserecalibration - command: nextflow run main.nf -profile test,recalibrate_bam,skip_bqsr --tools strelka --outdir results - tags: - - input_bam - - recalibrate - - preprocessing - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: 4d0effd3d8dc2b814230a189e7ca9dba - - path: results/multiqc - - path: results/preprocessing/converted/test/test.converted.cram - # binary changes md5sums on reruns - - path: results/preprocessing/converted/test/test.converted.cram.crai - # binary changes md5sums on reruns - - path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary - md5sum: 39ff2cc8eb7495a14a6b76e0ab627027 - - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count - md5sum: ee7dafc8d941b8502a04a63dc3126fff - - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual - contains: ["0 0 0 -nan 3 4 0.75", "2 0 1 0 2 4 0.5", "5 1 1 1 2 3 0.666667"] - - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/csv/recalibrated.csv - should_exist: false - - path: results/preprocessing/recal_table/test/test.recal.table - should_exist: false - - path: results/preprocessing/recalibrated/test/test.recal.cram - should_exist: false - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - should_exist: false - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - should_exist: false - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - should_exist: false - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - should_exist: false - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - should_exist: false - - path: results/reports/samtools/test/test.recal.cram.stats - should_exist: false - - path: results/preprocessing/mapped/ - should_exist: false - - path: results/preprocessing/markduplicates/ - should_exist: false diff --git a/tests/test_recalibrate_from_cram.yml b/tests/test_recalibrate_from_cram.yml deleted file mode 100644 index 9e53da4f2d..0000000000 --- a/tests/test_recalibrate_from_cram.yml +++ /dev/null @@ -1,78 +0,0 @@ -- name: Run Recalibration starting from cram - command: nextflow run main.nf -profile test,recalibrate_cram --outdir results - tags: - - input_cram - - recalibrate - - preprocessing - files: - - path: results/csv/recalibrated.csv - md5sum: 1888a924bc70bd80165a96ad641e22d6 - - path: results/multiqc - - path: results/preprocessing/recalibrated/test/test.recal.cram - # binary changes md5sums on reruns - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - # binary changes md5sums on reruns - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - - path: results/reports/samtools/test/test.recal.cram.stats - # conda changes md5sums for test - - path: results/preprocessing/mapped/ - should_exist: false - - path: results/preprocessing/markduplicates/ - should_exist: false -- name: Run Recalibration starting from cram and skip baserecalibration - command: nextflow run main.nf -profile test,recalibrate_cram,skip_bqsr --tools strelka --outdir results - tags: - - input_cram - - recalibrate - - preprocessing - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: 4d0effd3d8dc2b814230a189e7ca9dba - - path: results/multiqc - - path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary - md5sum: 39ff2cc8eb7495a14a6b76e0ab627027 - - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count - md5sum: ee7dafc8d941b8502a04a63dc3126fff - - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual - contains: ["0 0 0 -nan 3 4 0.75", "2 0 1 0 2 4 0.5", "5 1 1 1 2 3 0.666667"] - - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/csv/recalibrated.csv - should_exist: false - - path: results/preprocessing/markduplicates/test/test.md.cram - should_exist: false - - path: results/preprocessing/markduplicates/test/test.md.cram.crai - should_exist: false - - path: results/preprocessing/recal_table/test/test.recal.table - should_exist: false - - path: results/preprocessing/recalibrated/test/test.recal.cram - should_exist: false - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - should_exist: false - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - should_exist: false - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - should_exist: false - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - should_exist: false - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - should_exist: false - - path: results/reports/samtools/test/test.recal.cram.stats - should_exist: false - - path: results/preprocessing/mapped/ - should_exist: false - - path: results/preprocessing/markduplicates/ - should_exist: false diff --git a/tests/test_strelka.yml b/tests/test_strelka.yml deleted file mode 100644 index 57ddd2d67b..0000000000 --- a/tests/test_strelka.yml +++ /dev/null @@ -1,315 +0,0 @@ -- name: Skip variant calling on matched normal - command: nextflow run main.nf -profile test,variantcalling_channels --tools strelka --only_paired_variant_calling --outdir results - tags: - - somatic - - strelka - - variantcalling_channel - files: - - path: results/multiqc - - path: results/reports/bcftools/strelka/sample1/sample1.strelka.variants.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample2/sample2.strelka.variants.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample1/sample1.strelka.variants.FILTER.summary - md5sum: 2048a5de0201a6052c988a0189979a5f - - path: results/reports/vcftools/strelka/sample1/sample1.strelka.variants.TsTv.count - md5sum: c5b7a8eda2526d899098439ae4c06a49 - - path: results/reports/vcftools/strelka/sample1/sample1.strelka.variants.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.FILTER.summary - md5sum: fa3112841a4575d104916027c8851b30 - - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.TsTv.count - md5sum: d7f54d09d38af01a574a4930af21cfc9 - - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.TsTv.qual - contains: - [ - "19 453 47848 0.00946748 11 50 0.22", - "56 456 47875 0.0095248 8 25 0.32", - "72 458 47880 0.00956558 6 20 0.3", - "314 463 47899 0.00966617 1 1 1", - ] - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.FILTER.summary - md5sum: 3441628cd6550ed459ca1c3db989ceea - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.TsTv.count - md5sum: 8dcfdbcaac118df1d5ad407dd2af699f - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.FILTER.summary - md5sum: 4fc17fa5625b4d1dcc5d791b1eb22d85 - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.TsTv.count - md5sum: fc7af1f534890c4ad3025588b3af62ae - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.TsTv.qual - # conda changes md5sums for test - - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample2/sample2.strelka.genome.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample2/sample2.strelka.variants.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/sample3/strelka/sample3.strelka.variants.vcf.gz - should_exist: false - - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz.tbi - should_exist: false - - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz - should_exist: false - - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi - should_exist: false - - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - - path: results/reports/samtools/sample1/sample1.recal.cram.stats - - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz - - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi - - path: results/reports/samtools/sample2/sample2.recal.cram.stats - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - - path: results/reports/samtools/sample3/sample3.recal.cram.stats - # conda changes md5sums for test - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - - path: results/reports/samtools/sample4/sample4.recal.cram.stats - # conda changes md5sums for test -- name: Run variant calling on germline sample with strelka - command: nextflow run main.nf -profile test,tools_germline --tools strelka --outdir results - tags: - - germline - - strelka - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: cd8a47dfc3e44c395e9f693770ccc6c9 - - path: results/multiqc - - path: results/reports/bcftools/strelka/sample1/sample1.strelka.variants.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample1/sample1.strelka.variants.FILTER.summary - md5sum: 2048a5de0201a6052c988a0189979a5f - - path: results/reports/vcftools/strelka/sample1/sample1.strelka.variants.TsTv.count - md5sum: c5b7a8eda2526d899098439ae4c06a49 - - path: results/reports/vcftools/strelka/sample1/sample1.strelka.variants.TsTv.qual - # conda changes md5sums for test - - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/strelka - should_exist: false - - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz - - path: results/reports/mosdepth/sample1/sample1.recal.regions.bed.gz.csi - - path: results/reports/samtools/sample1/sample1.recal.cram.stats -- name: Run variant calling on germline sample with strelka without intervals - command: nextflow run main.nf -profile test,tools_germline --tools strelka --no_intervals --outdir results - tags: - - germline - - strelka - - no_intervals - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: cd8a47dfc3e44c395e9f693770ccc6c9 - - path: results/multiqc - - path: results/no_intervals.bed - md5sum: f3dac01ea66b95fe477446fde2d31489 - - path: results/no_intervals.bed.gz - md5sum: f3dac01ea66b95fe477446fde2d31489 - - path: results/no_intervals.bed.gz.tbi - md5sum: f3dac01ea66b95fe477446fde2d31489 - - path: results/reports/bcftools/strelka/sample1/sample1.strelka.variants.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample1/sample1.strelka.variants.FILTER.summary - md5sum: 2b7be6ff481fddc655210b836587810d - - path: results/reports/vcftools/strelka/sample1/sample1.strelka.variants.TsTv.count - md5sum: 1481854d2a765f5641856ecf95ca4097 - - path: results/reports/vcftools/strelka/sample1/sample1.strelka.variants.TsTv.qual - # conda changes md5sums for test - - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample1/sample1.strelka.genome.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample1/sample1.strelka.variants.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/strelka - should_exist: false - - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample1/sample1.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz - - path: results/reports/mosdepth/sample1/sample1.recal.per-base.bed.gz.csi - - path: results/reports/samtools/sample1/sample1.recal.cram.stats -- name: Run variant calling on somatic sample with strelka - command: nextflow run main.nf -profile test,tools_somatic --tools strelka --outdir results - tags: - - somatic - - strelka - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: 31ccee9472fed8bd15798724c62aee15 - - path: results/multiqc - - path: results/reports/bcftools/strelka/sample3/sample3.strelka.variants.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.FILTER.summary - md5sum: 2048a5de0201a6052c988a0189979a5f - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.TsTv.count - md5sum: c5b7a8eda2526d899098439ae4c06a49 - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.FILTER.summary - md5sum: 3441628cd6550ed459ca1c3db989ceea - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.TsTv.count - md5sum: 8dcfdbcaac118df1d5ad407dd2af699f - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.FILTER.summary - md5sum: 4fc17fa5625b4d1dcc5d791b1eb22d85 - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.TsTv.count - md5sum: fc7af1f534890c4ad3025588b3af62ae - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.TsTv.qual - # conda changes md5sums for test - - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/strelka - should_exist: false - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - - path: results/reports/samtools/sample3/sample3.recal.cram.stats - # conda changes md5sums for test - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - - path: results/reports/samtools/sample4/sample4.recal.cram.stats - # conda changes md5sums for test -- name: Run variant calling on somatic sample with strelka without intervals - command: nextflow run main.nf -profile test,tools_somatic --tools strelka --no_intervals --outdir results - tags: - - no_intervals - - somatic - - strelka - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: 31ccee9472fed8bd15798724c62aee15 - - path: results/multiqc - - path: results/no_intervals.bed - md5sum: f3dac01ea66b95fe477446fde2d31489 - - path: results/no_intervals.bed.gz - md5sum: f3dac01ea66b95fe477446fde2d31489 - - path: results/no_intervals.bed.gz.tbi - md5sum: f3dac01ea66b95fe477446fde2d31489 - - path: results/reports/bcftools/strelka/sample3/sample3.strelka.variants.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.FILTER.summary - md5sum: 2b7be6ff481fddc655210b836587810d - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.TsTv.count - md5sum: 1481854d2a765f5641856ecf95ca4097 - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.FILTER.summary - md5sum: 3441628cd6550ed459ca1c3db989ceea - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.TsTv.count - md5sum: 8dcfdbcaac118df1d5ad407dd2af699f - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.FILTER.summary - md5sum: 7a81b11aa29fec73d5bc872b7b58f8aa - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.TsTv.count - md5sum: a922c51ca3b2ea7cdcfa09e9c8c55d52 - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.TsTv.qual - # conda changes md5sums for test - - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/strelka - should_exist: false - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz - - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi - - path: results/reports/samtools/sample3/sample3.recal.cram.stats - # conda changes md5sums for test - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz - - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi - - path: results/reports/samtools/sample4/sample4.recal.cram.stats - # conda changes md5sums for test diff --git a/tests/test_strelka_bp.yml b/tests/test_strelka_bp.yml deleted file mode 100644 index f5954de37c..0000000000 --- a/tests/test_strelka_bp.yml +++ /dev/null @@ -1,213 +0,0 @@ -- name: Run variant calling on somatic sample with Strelka BP - command: nextflow run main.nf -profile test,tools_somatic --tools strelka,manta --outdir results - tags: - - somatic - - strelka_bp - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: eff248896ca462b76c79749403e44f48 - - path: results/multiqc - - path: results/reports/bcftools/manta/sample3/sample3.manta.diploid_sv.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample3/sample3.strelka.variants.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/vcftools/manta/sample3/sample3.manta.diploid_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample3/sample3.manta.diploid_sv.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/manta/sample3/sample3.manta.diploid_sv.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.TsTv.count - md5sum: 8dcfdbcaac118df1d5ad407dd2af699f - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.FILTER.summary - md5sum: 2048a5de0201a6052c988a0189979a5f - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.TsTv.count - md5sum: c5b7a8eda2526d899098439ae4c06a49 - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.FILTER.summary - md5sum: 3441628cd6550ed459ca1c3db989ceea - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.TsTv.count - md5sum: 8dcfdbcaac118df1d5ad407dd2af699f - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.FILTER.summary - md5sum: 4fc17fa5625b4d1dcc5d791b1eb22d85 - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.TsTv.count - md5sum: fc7af1f534890c4ad3025588b3af62ae - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.TsTv.qual - # conda changes md5sums for test - - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/manta - should_exist: false - - path: results/strelka - should_exist: false - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz - - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi - - path: results/reports/samtools/sample3/sample3.recal.cram.stats - # conda changes md5sums for test - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz - - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi - - path: results/reports/samtools/sample4/sample4.recal.cram.stats - # conda changes md5sums for test -- name: Run variant calling on somatic sample with Strelka BP without intervals - command: nextflow run main.nf -profile test,tools_somatic --tools strelka,manta --no_intervals --outdir results - tags: - - no_intervals - - somatic - - strelka_bp - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: eff248896ca462b76c79749403e44f48 - - path: results/multiqc - - path: results/no_intervals.bed - md5sum: f3dac01ea66b95fe477446fde2d31489 - - path: results/no_intervals.bed.gz - md5sum: f3dac01ea66b95fe477446fde2d31489 - - path: results/no_intervals.bed.gz.tbi - md5sum: f3dac01ea66b95fe477446fde2d31489 - - path: results/reports/bcftools/manta/sample3/sample3.manta.diploid_sv.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample3/sample3.strelka.variants.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt - # conda changes md5sums for test - - path: results/reports/vcftools/manta/sample3/sample3.manta.diploid_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample3/sample3.manta.diploid_sv.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/manta/sample3/sample3.manta.diploid_sv.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.TsTv.count - md5sum: 8dcfdbcaac118df1d5ad407dd2af699f - - path: results/reports/vcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.FILTER.summary - md5sum: 2b7be6ff481fddc655210b836587810d - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.TsTv.count - md5sum: 1481854d2a765f5641856ecf95ca4097 - - path: results/reports/vcftools/strelka/sample3/sample3.strelka.variants.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.FILTER.summary - md5sum: 3441628cd6550ed459ca1c3db989ceea - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.TsTv.count - md5sum: 8dcfdbcaac118df1d5ad407dd2af699f - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.TsTv.qual - # conda changes md5sums for test - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.FILTER.summary - md5sum: 7a81b11aa29fec73d5bc872b7b58f8aa - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.TsTv.count - md5sum: a922c51ca3b2ea7cdcfa09e9c8c55d52 - - path: results/reports/vcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.TsTv.qual - # conda changes md5sums for test - - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/manta/sample3/sample3.manta.diploid_sv.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz - # binary changes md5sums on reruns - - path: results/variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi - # binary changes md5sums on reruns - - path: results/manta - should_exist: false - - path: results/strelka - should_exist: false - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz - - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi - - path: results/reports/samtools/sample3/sample3.recal.cram.stats - # conda changes md5sums for test - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt - - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt - - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz - - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi - - path: results/reports/samtools/sample4/sample4.recal.cram.stats - # conda changes md5sums for test diff --git a/tests/tumor-normal-pair.nf.test.snap b/tests/tumor-normal-pair.nf.test.snap index 81892489a2..d9d38bee39 100644 --- a/tests/tumor-normal-pair.nf.test.snap +++ b/tests/tumor-normal-pair.nf.test.snap @@ -331,7 +331,6 @@ "samtools-stats-dp.txt:md5,d81e84864ecb732951a137e88d87a263", "samtools_alignment_plot.txt:md5,e757696d1f7107df2bd4ad92f607272e", "vcftools_tstv_by_count.txt:md5,9d3f23467779f62d81573894f71ba0d4", - "vcftools_tstv_by_qual.txt:md5,cc9762c7d4ee91803d358d8c386819d9", "test.strelka.variants.bcftools_stats.txt:md5,550430d0b8336ac650b7e50bdfdc914c", "test2_vs_test.strelka.somatic_indels.bcftools_stats.txt:md5,2ce8bffbfbb88c4da6a5239b11dc2f44", "test2_vs_test.strelka.somatic_snvs.bcftools_stats.txt:md5,869e2d3a46760e2bea9b2e027002848d", @@ -361,13 +360,10 @@ "test2.recal.cram.stats:md5,47c5ad8a7d4221d03673fd67388f9960", "test.strelka.variants.FILTER.summary:md5,dd87f507da7de20d5318841af312493b", "test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a", - "test.strelka.variants.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883", "test2_vs_test.strelka.somatic_indels.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423", "test2_vs_test.strelka.somatic_indels.TsTv.count:md5,8dcfdbcaac118df1d5ad407dd2af699f", - "test2_vs_test.strelka.somatic_indels.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883", "test2_vs_test.strelka.somatic_snvs.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423", - "test2_vs_test.strelka.somatic_snvs.TsTv.count:md5,8dcfdbcaac118df1d5ad407dd2af699f", - "test2_vs_test.strelka.somatic_snvs.TsTv.qual:md5,bc68ae4e688e9fb772b457069e604883" + "test2_vs_test.strelka.somatic_snvs.TsTv.count:md5,8dcfdbcaac118df1d5ad407dd2af699f" ], [ [ @@ -390,8 +386,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.09.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-10-08T12:12:19.788733" + "timestamp": "2024-11-09T18:22:56.125003" } } \ No newline at end of file diff --git a/tests/variant_calling_strelka.nf.test b/tests/variant_calling_strelka.nf.test new file mode 100644 index 0000000000..0411c409fc --- /dev/null +++ b/tests/variant_calling_strelka.nf.test @@ -0,0 +1,215 @@ +nextflow_pipeline { + + name "Test pipeline" + script "../main.nf" + tag "pipeline" + tag "pipeline_sarek" + + test("Run with profile test | --tools strelka --only_paired_variant_calling") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta' + fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai' + intervals = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed' + input = "${projectDir}/tests/csv/3.0/recalibrated.csv" + outdir = "$outputDir" + step = "variant_calling" + tools = 'strelka' + only_paired_variant_calling = true + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Run with profile test | --tools strelka | germline") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta' + fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai' + intervals = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed' + input = "${projectDir}/tests/csv/3.0/recalibrated_germline.csv" + outdir = "$outputDir" + step = "variant_calling" + tools = 'strelka' + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Run with profile test | --tools strelka --no_intervals | germline") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta' + fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai' + intervals = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed' + input = "${projectDir}/tests/csv/3.0/recalibrated_germline.csv" + outdir = "$outputDir" + no_intervals = true + step = "variant_calling" + tools = 'strelka' + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Run with profile test | --tools strelka | somatic") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta' + fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai' + intervals = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed' + input = "${projectDir}/tests/csv/3.0/recalibrated_somatic.csv" + outdir = "$outputDir" + step = "variant_calling" + tools = 'strelka' + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Run with profile test | --tools strelka --no_intervals | somatic") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta' + fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai' + intervals = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed' + input = "${projectDir}/tests/csv/3.0/recalibrated_somatic.csv" + outdir = "$outputDir" + no_intervals = true + step = "variant_calling" + tools = 'strelka' + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } +} diff --git a/tests/variant_calling_strelka.nf.test.snap b/tests/variant_calling_strelka.nf.test.snap new file mode 100644 index 0000000000..bf8ed3bc8d --- /dev/null +++ b/tests/variant_calling_strelka.nf.test.snap @@ -0,0 +1,835 @@ +{ + "Run with profile test | --tools strelka --only_paired_variant_calling": { + "content": [ + 26, + { + "BCFTOOLS_STATS": { + "bcftools": 1.2 + }, + "STRELKA_SINGLE": { + "strelka": "2.9.10" + }, + "STRELKA_SOMATIC": { + "strelka": "2.9.10" + }, + "VCFTOOLS_TSTV_COUNT": { + "vcftools": "0.1.16" + }, + "Workflow": { + "nf-core/sarek": "v3.5.0dev" + } + }, + [ + "csv", + "csv/variantcalled.csv", + 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| somatic") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta' + fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai' + intervals = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed' + input = "${projectDir}/tests/csv/3.0/recalibrated_somatic.csv" + outdir = "$outputDir" + step = "variant_calling" + tools = 'manta,strelka' + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } + + test("Run with profile test | --tools manta,strelka --no_intervals | somatic") { + + when { + params { + modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/' + fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta' + fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai' + intervals = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed' + input = "${projectDir}/tests/csv/3.0/recalibrated_somatic.csv" + outdir = "$outputDir" + no_intervals = true + step = "variant_calling" + tools = 'manta,strelka' + } + } + + 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 ${params.outdir}/ with stable content + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // cram_files: All cram files + def cram_files = getAllFilesFromDir(params.outdir, include: ['**/*.cram']) + def fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta' + assertAll( + { assert workflow.success}, + { assert snapshot( + // Number of successful tasks + workflow.trace.succeeded().size(), + // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions + removeNextflowVersion("$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 cram files + cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] } + ).match() } + ) + } + } +} diff --git a/tests/variant_calling_strelka_bp.nf.test.snap b/tests/variant_calling_strelka_bp.nf.test.snap new file mode 100644 index 0000000000..1ab795aa31 --- /dev/null +++ b/tests/variant_calling_strelka_bp.nf.test.snap @@ -0,0 +1,443 @@ +{ + "Run with profile test | --tools manta,strelka --no_intervals | somatic": { + "content": [ + 34, + { + "BCFTOOLS_STATS": { + "bcftools": 1.2 + }, + "MANTA_GERMLINE": { + "manta": "1.6.0" + }, + "MANTA_SOMATIC": { + "manta": "1.6.0" + }, + "STRELKA_SINGLE": { + "strelka": "2.9.10" + }, + "STRELKA_SOMATIC": { + "strelka": "2.9.10" + }, + "VCFTOOLS_TSTV_COUNT": { + "vcftools": "0.1.16" + }, + "Workflow": { + "nf-core/sarek": "v3.5.0dev" + } + }, + [ + "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", + 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"variant_calling/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.vcf.gz.tbi", + "variant_calling/strelka", + "variant_calling/strelka/sample3", + "variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz", + "variant_calling/strelka/sample3/sample3.strelka.genome.vcf.gz.tbi", + "variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz", + "variant_calling/strelka/sample3/sample3.strelka.variants.vcf.gz.tbi", + "variant_calling/strelka/sample4_vs_sample3", + "variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz", + "variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.vcf.gz.tbi", + "variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz", + "variant_calling/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.vcf.gz.tbi" + ], + [ + "bcftools-stats-subtypes.txt:md5,3bd8ab52708f28306c9cf9d2779c1715", + "bcftools_stats_indel-lengths.txt:md5,a836b904ccf4fa2a733a26b0184a5f9e", + "bcftools_stats_variant_depths.txt:md5,b4360600be4ee46148d30c428ec9e330", + "bcftools_stats_vqc_Count_Indels.txt:md5,def7f6a03fac61287483a7c86d44fe49", + "bcftools_stats_vqc_Count_SNP.txt:md5,a014a7c6d4fb7bea63e89da4cfeef2a9", + "bcftools_stats_vqc_Count_Transitions.txt:md5,ec192419e14a2aeb0c18742879bef563", + "bcftools_stats_vqc_Count_Transversions.txt:md5,b7ca7c37370d2db7052efe21c41d81e9", + "multiqc_bcftools_stats.txt:md5,97bac5dbfe6cb21a78ca7f7327655b65", + "multiqc_citations.txt:md5,ac2b3cf2dfb12c40837b9bbad8112d86", + "vcftools_tstv_by_count.txt:md5,27388870c36896df470e2f5aa982332e", + "sample3.manta.diploid_sv.bcftools_stats.txt:md5,8adad91e1c8dc8db63cf9b3607bee3a0", + "sample4_vs_sample3.manta.diploid_sv.bcftools_stats.txt:md5,17dc847445b98885bc18622f862f44d9", + "sample4_vs_sample3.manta.somatic_sv.bcftools_stats.txt:md5,a8660b352950f0b32768fcbbd6b48896", + "sample3.strelka.variants.bcftools_stats.txt:md5,d505d381e8c3906788e4135bb975ff84", + "sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt:md5,1c57e5cd6424157536276002ef1a58d6", + "sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt:md5,8cf6d0b3f41436cd2f2aa09c9831764d", + "sample3.recal.mosdepth.global.dist.txt:md5,d9a4dd6429560b2b647da346050766c5", + "sample3.recal.mosdepth.region.dist.txt:md5,1f3dab381958e08eb00f7c5e1135f677", + "sample3.recal.mosdepth.summary.txt:md5,d7676e7c1de851b0ee5185d21096123b", + "sample3.recal.regions.bed.gz:md5,6edeb8f7041a4403cb73651744b5bc82", + "sample3.recal.regions.bed.gz.csi:md5,f17cc9d960aa4a1e96548d570585cc8a", + "sample4.recal.mosdepth.global.dist.txt:md5,53f9ae9ab5002ffba340fa8cef7d70e4", + "sample4.recal.mosdepth.region.dist.txt:md5,17600d21ac453506c52249cf435ad8ea", + "sample4.recal.mosdepth.summary.txt:md5,7141030385af1f653718c9e0c9a5be80", + "sample4.recal.regions.bed.gz:md5,c680c5d75f0cea068e3f917f4cf9bf52", + "sample4.recal.regions.bed.gz.csi:md5,4003c8833ed5e9b9f45282a6915c935e", + "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b", + "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03", + "sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423", + "sample3.manta.diploid_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a", + "sample4_vs_sample3.manta.diploid_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423", + "sample4_vs_sample3.manta.diploid_sv.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a", + "sample4_vs_sample3.manta.somatic_sv.FILTER.summary:md5,1ce42d34e4ae919afb519efc99146423", + "sample4_vs_sample3.manta.somatic_sv.TsTv.count:md5,8dcfdbcaac118df1d5ad407dd2af699f", + "sample3.strelka.variants.FILTER.summary:md5,fef8aeadd3b0f3b8c040c0da03bf1cbd", + "sample3.strelka.variants.TsTv.count:md5,c5b7a8eda2526d899098439ae4c06a49", + "sample4_vs_sample3.strelka.somatic_indels.FILTER.summary:md5,30a45e2bc87f40c89388032cbf75ec65", + "sample4_vs_sample3.strelka.somatic_indels.TsTv.count:md5,8dcfdbcaac118df1d5ad407dd2af699f", + "sample4_vs_sample3.strelka.somatic_snvs.FILTER.summary:md5,4fc17fa5625b4d1dcc5d791b1eb22d85", + "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,fc7af1f534890c4ad3025588b3af62ae" + ], + [ + + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.10.0" + }, + "timestamp": "2024-11-15T22:37:23.231917992" + } +} \ No newline at end of file diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf index d756ce0512..ae7805fe59 100644 --- a/workflows/sarek/main.nf +++ b/workflows/sarek/main.nf @@ -41,7 +41,6 @@ include { FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON } from '../../subwor include { BAM_MERGE_INDEX_SAMTOOLS } from '../../subworkflows/local/bam_merge_index_samtools/main' // Convert BAM files -include { SAMTOOLS_CONVERT as BAM_TO_CRAM } from '../../modules/nf-core/samtools/convert/main' include { SAMTOOLS_CONVERT as BAM_TO_CRAM_MAPPING } from '../../modules/nf-core/samtools/convert/main' // Convert CRAM files (optional) @@ -387,16 +386,7 @@ workflow SAREK { if (params.step == 'mapping') { cram_skip_markduplicates = BAM_TO_CRAM_MAPPING.out.cram.join(BAM_TO_CRAM_MAPPING.out.crai, failOnDuplicate: true, failOnMismatch: true) } else { - input_markduplicates_convert = input_sample.branch{ - bam: it[0].data_type == "bam" - cram: it[0].data_type == "cram" - } - - // Convert any input BAMs to CRAM - BAM_TO_CRAM(input_markduplicates_convert.bam, fasta, fasta_fai) - versions = versions.mix(BAM_TO_CRAM.out.versions) - - cram_skip_markduplicates = Channel.empty().mix(input_markduplicates_convert.cram, BAM_TO_CRAM.out.cram.join(BAM_TO_CRAM.out.crai, failOnDuplicate: true, failOnMismatch: true)) + cram_skip_markduplicates = Channel.empty().mix(input_sample) } CRAM_QC_NO_MD(cram_skip_markduplicates, fasta, intervals_for_preprocessing) @@ -478,22 +468,10 @@ workflow SAREK { // Run if starting from step "prepare_recalibration" if (params.step == 'prepare_recalibration') { - // Support if starting from BAM or CRAM files - input_prepare_recal_convert = input_sample.branch{ - bam: it[0].data_type == "bam" - cram: it[0].data_type == "cram" - } - - // BAM files first must be converted to CRAM files since from this step on we base everything on CRAM format - BAM_TO_CRAM(input_prepare_recal_convert.bam, fasta, fasta_fai) - versions = versions.mix(BAM_TO_CRAM.out.versions) + ch_cram_for_bam_baserecalibrator = Channel.empty().mix(input_sample) - ch_cram_from_bam = BAM_TO_CRAM.out.cram.join(BAM_TO_CRAM.out.crai, failOnDuplicate: true, failOnMismatch: true) - // Make sure correct data types are carried through - .map{ meta, cram, crai -> [ meta + [data_type: "cram"], cram, crai ] } - - ch_cram_for_bam_baserecalibrator = Channel.empty().mix(ch_cram_from_bam, input_prepare_recal_convert.cram) - ch_md_cram_for_restart = ch_cram_from_bam + // Set the input samples for restart so we generate a samplesheet that contains the input files together with the recalibration table + ch_md_cram_for_restart = ch_cram_for_bam_baserecalibrator } else { @@ -567,27 +545,8 @@ workflow SAREK { // Run if starting from step "prepare_recalibration" if (params.step == 'recalibrate') { - // Support if starting from BAM or CRAM files - input_recal_convert = input_sample.branch{ - bam: it[0].data_type == "bam" - cram: it[0].data_type == "cram" - } - - // If BAM file, split up table and mapped file to convert BAM to CRAM - input_only_table = input_recal_convert.bam.map{ meta, bam, bai, table -> [ meta, table ] } - input_only_bam = input_recal_convert.bam.map{ meta, bam, bai, table -> [ meta, bam, bai ] } - - // BAM files first must be converted to CRAM files since from this step on we base everything on CRAM format - BAM_TO_CRAM(input_only_bam, fasta, fasta_fai) - versions = versions.mix(BAM_TO_CRAM.out.versions) + cram_applybqsr = Channel.empty().mix(input_sample) - cram_applybqsr = Channel.empty().mix( - BAM_TO_CRAM.out.cram.join(BAM_TO_CRAM.out.crai, failOnDuplicate: true, failOnMismatch: true) - .join(input_only_table, failOnDuplicate: true, failOnMismatch: true), - - input_recal_convert.cram) - // Join together converted cram with input tables - .map{ meta, cram, crai, table -> [ meta + [data_type: "cram"], cram, crai, table ]} } if (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator'))) { @@ -642,9 +601,7 @@ workflow SAREK { // cram_variant_calling contains either: // - input bams converted to crams, if started from step recal + skip BQSR // - input crams if started from step recal + skip BQSR - cram_variant_calling = Channel.empty().mix( - BAM_TO_CRAM.out.cram.join(BAM_TO_CRAM.out.crai, failOnDuplicate: true, failOnMismatch: true), - input_recal_convert.cram.map{ meta, cram, crai, table -> [ meta, cram, crai ] }) + cram_variant_calling = Channel.empty().mix(input_sample.map{ meta, cram, crai, table -> [ meta, cram, crai ] }) } else { // cram_variant_calling contains either: // - crams from markduplicates = ch_cram_for_bam_baserecalibrator if skip BQSR but not started from step recalibration @@ -654,19 +611,7 @@ workflow SAREK { if (params.step == 'variant_calling') { - input_variant_calling_convert = input_sample.branch{ - bam: it[0].data_type == "bam" - cram: it[0].data_type == "cram" - } - - // BAM files first must be converted to CRAM files since from this step on we base everything on CRAM format - BAM_TO_CRAM(input_variant_calling_convert.bam, fasta, fasta_fai) - versions = versions.mix(BAM_TO_CRAM.out.versions) - - cram_variant_calling = Channel.empty().mix( - BAM_TO_CRAM.out.cram.join(BAM_TO_CRAM.out.crai, failOnDuplicate: true, failOnMismatch: true), - input_variant_calling_convert.cram - ) + cram_variant_calling = Channel.empty().mix( input_sample ) }