diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 8a2d96f13b..c58128e68a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -2,15 +2,12 @@ name: nf-core CI # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors on: push: - branches: - - dev + branches: [dev] pull_request: release: types: [published] -env: - NXF_ANSI_LOG: false - +# Cancel if a newer run is started concurrency: group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} cancel-in-progress: true @@ -34,9 +31,11 @@ jobs: exclude: - NXF_VER: "latest-everything" profile: "conda" + env: + NXF_ANSI_LOG: false steps: - name: Check out pipeline code - uses: actions/checkout@v2 + uses: actions/checkout@v3 - name: Set up Python uses: actions/setup-python@v2 @@ -107,88 +106,3 @@ jobs: /home/runner/pytest_workflow_*/*/work !/home/runner/pytest_workflow_*/*/work/conda !/home/runner/pytest_workflow_*/*/work/singularity - - test_all: - name: Run pipeline with test data (complete) - # Only run on push if this is the nf-core dev branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/sarek') }}" - runs-on: ubuntu-latest - strategy: - # HACK Remove after DSL2 rewrite is done - fail-fast: false - matrix: - NXF_VER: - - "21.10.3" - test: - - "aligner" - - "alignment_to_fastq" - - "annotation" - - "cnvkit" - - "controlfreec" - - "deepvariant" - - "freebayes" - - "gatk4_spark" - - "haplotypecaller" - - "intervals" - - "manta" - - "markduplicates" - - "mpileup" - - "msisensorpro" - - "mutect2" - - "prepare_recalibration" - - "recalibrate" - - "save_mapped" - - "save_output_as_bam" - - "skip_markduplicates" - - "skip_qc" - - "split_fastq" - - "strelka" - - "strelkabp" - - "targeted" - - "tiddit" - - "trimming" - - "tumor_normal_pair" - - "umi" - - "variantcalling_channel" - profile: ["docker"] - steps: - - name: Check out pipeline code - uses: actions/checkout@v2 - - - name: Install Nextflow - uses: nf-core/setup-nextflow@v1 - with: - version: "${{ matrix.NXF_VER }}" - - - name: Set up Python - uses: actions/setup-python@v2 - with: - python-version: "3.x" - - - name: Install dependencies - run: python -m pip install --upgrade pip pytest-workflow - - - name: Run pipeline with tests settings - uses: Wandalen/wretry.action@v1.0.11 - with: - command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.test }} --symlink --kwdof --git-aware --color=yes - attempt_limit: 3 - - - name: Output log on failure - if: failure() - run: | - sudo apt install bat > /dev/null - batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} - - - name: Upload logs on failure - if: failure() - uses: actions/upload-artifact@v2 - with: - name: logs-${{ matrix.profile }} - path: | - /home/runner/pytest_workflow_*/*/.nextflow.log - /home/runner/pytest_workflow_*/*/log.out - /home/runner/pytest_workflow_*/*/log.err - /home/runner/pytest_workflow_*/*/work - !/home/runner/pytest_workflow_*/*/work/conda - !/home/runner/pytest_workflow_*/*/work/singularity diff --git a/.github/workflows/pytest-workflow.yml b/.github/workflows/pytest-workflow.yml new file mode 100644 index 0000000000..ad93edfc35 --- /dev/null +++ b/.github/workflows/pytest-workflow.yml @@ -0,0 +1,130 @@ +name: pytest-workflow +# This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors +on: + pull_request: + branches: [dev] + +# Cancel if a newer run is started +concurrency: + group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} + cancel-in-progress: true + +jobs: + changes: + name: Check for changes + runs-on: ubuntu-latest + outputs: + # Expose matched filters as job 'tags' output variable + tags: ${{ steps.filter.outputs.changes }} + steps: + - uses: actions/checkout@v3 + - uses: dorny/paths-filter@v2 + id: filter + with: + filters: "tests/config/pytest_tags.yml" + + test: + name: ${{ matrix.tags }} ${{ matrix.profile }} + runs-on: ubuntu-latest + needs: changes + if: needs.changes.outputs.tags != '[]' + strategy: + fail-fast: false + matrix: + tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] + profile: ["docker", "singularity", "conda"] + NXF_VER: + - "21.10.3" + - "latest-everything" + exclude: + - profile: "conda" + NXF_VER: "latest-everything" + - profile: "conda" + tags: umi + - profile: "conda" + tags: deepvariant + - profile: "conda" + tags: haplotypecaller + - profile: "conda" + tags: merge + - profile: "conda" + tags: snpeff + - profile: "conda" + tags: vep + - profile: "singularity" + tags: merge + env: + NXF_ANSI_LOG: false + steps: + - name: Check out pipeline code + uses: actions/checkout@v3 + + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: "3.x" + + - uses: actions/cache@v2 + with: + path: ~/.cache/pip + key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }} + restore-keys: | + ${{ runner.os }}-pip- + + - name: Install Python dependencies + run: python -m pip install --upgrade pip pytest-workflow + + - uses: actions/cache@v2 + with: + path: /usr/local/bin/nextflow + key: ${{ runner.os }} + restore-keys: | + ${{ runner.os }}-nextflow- + + - name: Install Nextflow + uses: nf-core/setup-nextflow@v1 + with: + version: "${{ matrix.NXF_VER }}" + + - name: Set up Singularity + if: matrix.profile == 'singularity' + uses: eWaterCycle/setup-singularity@v5 + with: + singularity-version: 3.7.1 + + - name: Set up miniconda + if: matrix.profile == 'conda' + uses: conda-incubator/setup-miniconda@v2 + with: + auto-update-conda: true + channels: conda-forge,bioconda,defaults + python-version: ${{ matrix.python-version }} + + - name: Conda clean + if: matrix.profile == 'conda' + run: conda clean -a + + - name: Run pytest-workflow + uses: Wandalen/wretry.action@v1.0.11 + with: + command: TMPDIR=~ PROFILE=${{ matrix.profile }} pytest --tag ${{ matrix.tags }} --symlink --kwdof --git-aware --color=yes + attempt_limit: 3 + + - name: Output log on failure + if: failure() + run: | + sudo apt install bat > /dev/null + batcat --decorations=always --color=always /home/runner/pytest_workflow_*/*/log.{out,err} + + - name: Upload logs on failure + if: failure() + uses: actions/upload-artifact@v2 + with: + name: logs-${{ matrix.profile }} + path: | + /home/runner/pytest_workflow_*/*/.nextflow.log + /home/runner/pytest_workflow_*/*/log.out + /home/runner/pytest_workflow_*/*/log.err + /home/runner/pytest_workflow_*/*/work + !/home/runner/pytest_workflow_*/*/work/conda + !/home/runner/pytest_workflow_*/*/work/singularity diff --git a/.nf-core.yml b/.nf-core.yml index 4120c0234c..230681c724 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,5 +1,9 @@ repository_type: pipeline lint: + files_exist: + - conf/modules.config + - conf/test.config + - conf/test_full.config files_unchanged: - assets/multiqc_config.yml - assets/nf-core-sarek_logo_light.png diff --git a/conf/modules.config b/conf/modules.config deleted file mode 100644 index 096ebb8b37..0000000000 --- a/conf/modules.config +++ /dev/null @@ -1,1385 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Config file for defining DSL2 per module options and publishing paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Available keys to override module options: - ext.args = Additional arguments appended to command in module. - ext.args2 = Second set of arguments appended to command in module (multi-tool modules). - ext.args3 = Third set of arguments appended to command in module (multi-tool modules). - ext.prefix = File name prefix for output files. - ext.when = When to run the module. ----------------------------------------------------------------------------------------- -*/ - -process { - - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - - withName: CUSTOM_DUMPSOFTWAREVERSIONS { - cache = false - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/pipeline_info" }, - pattern: '*_versions.yml' - ] - } - -// PREPARE_GENOME - - withName: 'BWAMEM1_INDEX' { - ext.when = { !params.bwa && params.step == "mapping" && params.aligner == "bwa-mem" } - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference" }, - pattern: "bwa" - ] - } - - withName: 'BWAMEM2_INDEX' { - ext.when = { !params.bwamem2 && params.step == "mapping" && params.aligner == "bwa-mem2" } - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference" }, - pattern: "bwamem2" - ] - } - - withName: 'DRAGMAP_HASHTABLE' { - ext.when = { !params.dragmap && params.step == "mapping" && params.aligner == "dragmap" } - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference" }, - pattern: "dragmap" - ] - } - - withName: 'GATK4_CREATESEQUENCEDICTIONARY' { - ext.when = { !params.dict && params.step != "annotate" && params.step != "controlfreec" } - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/dict" }, - pattern: "*dict" - ] - } - - withName: 'MSISENSORPRO_SCAN' { - ext.when = { params.tools && params.tools.split(',').contains('msisensorpro') } - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/msi" }, - pattern: "*list" - ] - } - - withName: 'SAMTOOLS_FAIDX' { - ext.when = { !params.fasta_fai && params.step != "annotate" } - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/fai" }, - pattern: "*fai" - ] - } - - withName: 'TABIX_DBSNP' { - ext.when = { !params.dbsnp_tbi && params.dbsnp && (params.step == "mapping" || params.step == "markduplicates" || params.step == "prepare_recalibration") || params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('mutect2')) } - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/dbsnp" }, - pattern: "*vcf.gz.tbi" - ] - } - - withName: 'TABIX_GERMLINE_RESOURCE' { - ext.when = { !params.germline_resource_tbi && params.germline_resource && params.tools && params.tools.split(',').contains('mutect2') } - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/germline_resource" }, - pattern: "*vcf.gz.tbi" - ] - } - - withName: 'TABIX_KNOWN_INDELS' { - ext.when = { !params.known_indels_tbi && params.known_indels && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && params.tools.split(',').contains('haplotypecaller')) ) } - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/known_indels" }, - pattern: "*vcf.gz.tbi" - ] - } - - withName: 'TABIX_KNOWN_SNPS' { - ext.when = { !params.known_snps_tbi && params.known_snps && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && params.tools.split(',').contains('haplotypecaller')) ) } - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/known_snps" }, - pattern: "*vcf.gz.tbi" - ] - } - - withName: 'TABIX_PON' { - ext.when = { !params.pon_tbi && params.pon && params.tools && params.tools.split(',').contains('mutect2') } - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/pon" }, - pattern: "*vcf.gz.tbi" - ] - } - - withName: 'UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT' { - ext.when = { params.tools && params.tools.split(',').contains('ascat')} - publishDir = [ - enabled: false - ] - } - - withName: 'UNTAR_CHR_DIR' { - ext.when = { params.tools && params.tools.split(',').contains('controlfreec')} - } - - withName: 'CNVKIT_ANTITARGET' { - ext.when = { params.tools && params.tools.split(',').contains('cnvkit') } - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/cnvkit" }, - pattern: "*{bed}" - ] - } - - withName: 'CNVKIT_REFERENCE' { - ext.prefix = "cnvkit" - ext.when = { params.tools && params.tools.split(',').contains('cnvkit') } - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/cnvkit" }, - pattern: "*{cnn}" - ] - } - - -// PREPARE INTERVALS - - withName: 'CREATE_INTERVALS_BED' { - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/intervals" }, - pattern: "*bed" - ] - } - - withName: 'GATK4_INTERVALLISTTOBED' { - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/intervals" }, - pattern: "*bed" - ] - } - - withName: 'TABIX_BGZIPTABIX_INTERVAL_SPLIT' { - ext.prefix = {"${meta.id}"} - publishDir = [ - enabled: params.save_reference, - mode: params.publish_dir_mode, - path: { "${params.outdir}/reference/intervals" }, - pattern: "*bed.gz" - ] - } - -// BAM TO FASTQ - - withName: 'COLLATE_FASTQ_MAP' { - ext.args2 = '-N' - ext.prefix = {"${meta.id}.mapped"} - publishDir = [ - //specify to avoid publishing, overwritten otherwise - enabled: false - ] - } - - withName: 'COLLATE_FASTQ_UNMAP' { - ext.args2 = '-N' - ext.prefix = {"${meta.id}.unmapped"} - publishDir = [ - //specify to avoid publishing, overwritten otherwise - enabled: false - ] - } - - withName: 'SAMTOOLS_VIEW_MAP_MAP' { - ext.args = '-b -f1 -F12' - ext.prefix = {"${meta.id}.map_map"} - publishDir = [ - //specify to avoid publishing, overwritten otherwise - enabled: false - ] - } - - withName: 'SAMTOOLS_VIEW_MAP_UNMAP' { - ext.args = '-b -f8 -F260' - ext.prefix = {"${meta.id}.map_unmap"} - publishDir = [ - //specify to avoid publishing, overwritten otherwise - enabled: false - ] - } - - withName: 'SAMTOOLS_VIEW_UNMAP_MAP' { - ext.args = '-b -f4 -F264' - ext.prefix = {"${meta.id}.unmap_map"} - publishDir = [ - //specify to avoid publishing, overwritten otherwise - enabled: false - ] - } - - withName: 'SAMTOOLS_VIEW_UNMAP_UNMAP' { - ext.args = '-b -f12 -F256' - ext.prefix = {"${meta.id}.unmap_unmap"} - publishDir = [ - //specify to avoid publishing, overwritten otherwise - enabled: false - ] - } - - withName: 'SAMTOOLS_MERGE_UNMAP' { - ext.prefix = {"${meta.id}.merged_unmap"} - publishDir = [ - //specify to avoid publishing, overwritten otherwise - enabled: false - ] - } - withName: 'CAT_FASTQ' { - publishDir = [ - //specify to avoid publishing, overwritten otherwise - enabled: false - ] - } - -// TRIMMING - - withName: 'FASTP' { - ext.args = [ "", - params.trim_fastq ?: "--disable_adapter_trimming", - params.clip_r1 > 0 ? "--trim_front1 ${params.clip_r1}" : "", // Remove bp from the 5' end of read 1. - params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed. - params.clip_r2 > 0 ? "--trim_front2 ${params.clip_r2}" : "", //Remove bp from the 5' end of read 2. - params.three_prime_clip_r2 > 0 ? "--trim_tail2 ${params.three_prime_clip_r2}" : "", // Remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed. - params.trim_nextseq ? "--trim_poly_g" : "", // Apply the --nextseq=X option, to trim based on quality after removing poly-G tails. - params.split_fastq > 0 ? "--split_by_lines ${params.split_fastq * 4}" : "", - - ].join(" ").trim() - publishDir = [ - [ - path: { "${params.outdir}/reports/fastp/${meta.sample}" }, - mode: params.publish_dir_mode, - pattern: "*.{html,json,log}" - ], - [ - enabled: params.save_trimmed || params.save_split_fastqs, - path: { "${params.outdir}/preprocessing/fastp/${meta.sample}/" }, - mode: params.publish_dir_mode, - pattern: "*.fastp.fastq.gz" - ] - ] - } - -// UMI Subworkflow - - withName: 'FASTQTOBAM' { - ext.prefix = {"${meta.id}"} - ext.args = { "--read-structures $params.umi_read_structure" } - publishDir = [ - //specify to avoid publishing, overwritten otherwise - enabled: false - ] - } - - withName: 'BAM2FASTQ' { - ext.args = '-T RX' - ext.when = { params.umi_read_structure } - publishDir = [ - //specify to avoid publishing, overwritten otherwise - enabled: false - ] - } - - if (params.umi_read_structure) { - withName: "NFCORE_SAREK:SAREK:FASTQ_CREATE_UMI_CONSENSUS_FGBIO:ALIGN_UMI:BWAMEM.*_MEM" { - ext.args = { "-K 100000000 -p -C -Y -R ${meta.read_group}" } - ext.args2 = '-bS' - ext.prefix = {"${meta.id}.umi_unsorted"} - publishDir = [ - //specify to avoid publishing, overwritten otherwise - enabled: false - ] - } - - withName: "NFCORE_SAREK:SAREK:FASTQ_CREATE_UMI_CONSENSUS_FGBIO:ALIGN_UMI:DRAGMAP_ALIGN" { - ext.args2 = '-bS' - ext.prefix = {"${meta.id}.umi_unsorted"} - publishDir = [ - //specify to avoid publishing, overwritten otherwise - enabled: false - ] - } - } - - withName: 'SAMBLASTER' { - ext.args = '-M --addMateTags' - ext.prefix = {"${meta.id}_unsorted_tagged"} - publishDir = [ - //specify to avoid publishing, overwritten otherwise - enabled: false - ] - } - withName: 'GROUPREADSBYUMI' { - publishDir = [ - [ path: { "${params.outdir}/reports/umi/" }, - mode: params.publish_dir_mode, - pattern: "*.{txt}" - ] - ] - } - - withName: 'CALLUMICONSENSUS' { - ext.args = '-M 1 -S Coordinate' - ext.prefix = {"${meta.id}_umi-consensus"} - publishDir = [ - path: { "${params.outdir}/preprocessing/umi/${meta.sample}" }, - mode: params.publish_dir_mode, - pattern: "*.{bam}" - ] - } - -// MAPPING - - if (params.step == 'mapping') { - withName: "BWAMEM1_MEM" { - ext.when = { params.aligner == "bwa-mem" } - } - withName: "BWAMEM2_MEM" { - ext.when = { params.aligner == "bwa-mem2" } - } - - withName: "DRAGMAP_ALIGN" { - ext.when = { params.aligner == "dragmap" } - ext.args = { "--RGSM ${meta.read_group}" } - } - - withName: "(BWAMEM.*_MEM|DRAGMAP_ALIGN)" { - // Markduplicates Spark NEEDS name-sorted reads or runtime goes through the roof - // However if it's skipped, reads need to be coordinate-sorted - // Only name sort if Spark for Markduplicates + duplicate marking is not skipped - ext.args2 = { params.use_gatk_spark && params.use_gatk_spark.contains('markduplicates') && (!params.skip_tools || (params.skip_tools && !params.skip_tools.split(',').contains('markduplicates'))) ? '-n' : '' } - ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "${meta.id}.sorted" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/preprocessing/" }, - pattern: "*bam", - // Only save if (save_mapped OR (no_markduplicates AND save_output_as_bam)) AND only a single BAM file per sample - saveAs: { (params.save_output_as_bam && (params.save_mapped || params.skip_tools && params.skip_tools.split(',').contains('markduplicates'))) && (meta.size * meta.numLanes == 1) ? "mapped/${meta.id}/${it}" : null } - ] - } - - withName: "BWAMEM.*_MEM" { - // Using -B 3 for tumor samples - ext.args = { meta.status == 1 ? "-K 100000000 -Y -B 3 -R ${meta.read_group}" : "-K 100000000 -Y -R ${meta.read_group}" } - } - } - - withName: 'MERGE_BAM|INDEX_MERGE_BAM' { - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/preprocessing/" }, - pattern: "*{bam,bai}", - // Only save if (save_output_as_bam AND (no_markduplicates OR save_mapped )) - saveAs: { (params.save_output_as_bam && (params.save_mapped || params.skip_tools && params.skip_tools.split(',').contains('markduplicates'))) ? "mapped/${meta.id}/${it}" : null } - ] - } - - withName: 'MERGE_BAM' { - ext.prefix = { "${meta.id}.sorted" } - } - -// MARKDUPLICATES - - withName: 'CRAM_TO_BAM' { - ext.args = "-b" - } - - withName: 'BAM_TO_CRAM' { - // BAM provided for step Markduplicates either run through MD or Convert -> then saved as sorted.cram (convert) or md.cram (md directly) - // BAM files provided for step prepare_recal are converted and run through BQSR -> then saved as md.cram - // BAM files provided for step recal are converted and run through BQSR II -> then saved as md.cram - ext.args = "-C" - ext.prefix = { "${meta.id}.converted" } - publishDir = [ - enabled: !params.save_output_as_bam, - mode: params.publish_dir_mode, - path: { "${params.outdir}/preprocessing/converted/${meta.id}" }, - pattern: "*{cram,crai}" - ] - } - - withName: 'BAM_TO_CRAM_MAPPING' { - // Run only when mapping should be saved as CRAM or when no MD is done - ext.when = (params.save_mapped && !params.save_output_as_bam) || (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) - ext.prefix = { "${meta.id}.sorted" } - publishDir = [ - // Never publish if BAM only should be published - enabled: !params.save_output_as_bam, - mode: params.publish_dir_mode, - path: { "${params.outdir}/preprocessing/mapped/${meta.id}/" }, - pattern: "*{cram,crai}" - ] - } - - withName: 'GATK4_ESTIMATELIBRARYCOMPLEXITY' { - ext.prefix = { "${meta.id}.md.cram" } - ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates_report')) } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/reports/markduplicates/${meta.id}" }, - pattern: "*metrics" - ] - } - - withName: 'GATK4_MARKDUPLICATES' { - ext.args = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true' - ext.prefix = { "${meta.id}.md.cram" } - ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) } - publishDir = [ - [ - enabled: !params.save_output_as_bam, - mode: params.publish_dir_mode, - path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" }, - pattern: "*{cram,crai}" - ], - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/reports/" }, - pattern: "*metrics", - saveAs: { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates_report')) ? "markduplicates/${meta.id}/${it}" : null} - ] - ] - } - - withName: 'GATK4_MARKDUPLICATES_SPARK' { - ext.args = '--remove-sequencing-duplicates false -VS LENIENT' - ext.prefix = { "${meta.id}.md.cram" } - publishDir = [ - enabled: !params.save_output_as_bam, - mode: params.publish_dir_mode, - path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" }, - pattern: "*{cram,crai}" - ] - } - - withName: 'INDEX_MARKDUPLICATES' { - publishDir = [ - enabled: !params.save_output_as_bam, - mode: params.publish_dir_mode, - path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" }, - pattern: "*{cram,crai}" - ] - } - - - withName: 'NFCORE_SAREK:SAREK:CRAM_TO_BAM' { - ext.prefix = { "${meta.id}.md" } - ext.when = { params.save_output_as_bam } - publishDir = [ - enabled: params.save_output_as_bam, - mode: params.publish_dir_mode, - path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" }, - pattern: "*{md.bam,md.bam.bai}" - ] - } - -// PREPARE_RECALIBRATION - - withName: 'GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/preprocessing/" }, - pattern: "*table", - saveAs: { meta.num_intervals > 1 ? null : "recal_table/${meta.id}/${it}" } - ] - } - - withName: 'GATK4_GATHERBQSRREPORTS' { - ext.prefix = {"${meta.id}.recal"} - ext.when = { meta.num_intervals > 1 } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/preprocessing/recal_table/${meta.id}/" }, - pattern: "*table", - ] - } - -// RECALIBRATE - - withName: 'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" } - publishDir = [ - enabled: !params.save_output_as_bam, - mode: params.publish_dir_mode, - path: { "${params.outdir}/preprocessing/" }, - pattern: "*cram", - saveAs: { meta.num_intervals > 1 ? null : "recalibrated/${meta.id}/${it}" } - ] - } - - - if ((params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') && (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator')))) { - withName: 'NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM' { - ext.prefix = { "${meta.id}.recal" } - ext.when = { meta.num_intervals > 1 } - publishDir = [ - enabled: !params.save_output_as_bam, - mode: params.publish_dir_mode, - path: { "${params.outdir}/preprocessing/recalibrated/${meta.id}/" }, - pattern: "*cram" - ] - } - - withName: 'NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM' { - publishDir = [ - enabled: !params.save_output_as_bam, - mode: params.publish_dir_mode, - path: { "${params.outdir}/preprocessing/recalibrated/${meta.id}/" }, - pattern: "*{recal.cram,recal.cram.crai}" - ] - } - } - - withName: 'CRAM_TO_BAM_RECAL' { - ext.prefix = { "${meta.id}.recal" } - ext.when = { params.save_output_as_bam} - publishDir = [ - enabled: params.save_output_as_bam, - mode: params.publish_dir_mode, - path: { "${params.outdir}/preprocessing/recalibrated/${meta.id}/" }, - pattern: "*{recal.bam,recal.bam.bai}" - ] - } - -// QC - - withName: 'FASTQC' { - ext.args = '--quiet' - ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('fastqc')) } - publishDir = [ - [ - path: { "${params.outdir}/reports/fastqc/${meta.id}" }, - mode: params.publish_dir_mode, - pattern: "*{html,zip}" - ] - ] - } - - withName: 'NFCORE_SAREK:SAREK:(BAM_MARKDUPLICATES|BAM_MARKDUPLICATES_SPARK):CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS' { - ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) } - ext.prefix = { "${meta.id}.md.cram" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/reports/samtools/${meta.id}" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: 'NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS' { - ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) } - ext.prefix = { "${meta.id}.sorted.cram" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/reports/samtools/${meta.id}" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: 'MOSDEPTH' { - ext.args = { !params.wes ? "-n --fast-mode --by 500" : ""} - ext.prefix = { params.skip_tools && params.skip_tools.split(',').contains('markduplicates') ? "${meta.id}.sorted" : "${meta.id}.md" } - ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('mosdepth')) } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/reports/mosdepth/${meta.id}" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - ] - } - - if ((params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') && (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator')))) { - withName: 'NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH' { - ext.prefix = { "${meta.id}.recal" } - } - - withName: 'NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS' { - ext.prefix = { "${meta.id}.recal.cram" } - ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/reports/samtools/${meta.id}" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - } -} - -// VARIANT CALLING - -process{ - - // CNVKIT - withName: 'CNVKIT_BATCH' { - ext.args = { params.wes ? "--method hybrid --diagram --scatter" : "--method wgs --diagram --scatter" } - ext.when = { params.tools && params.tools.split(',').contains('cnvkit') } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" }, - pattern: "*{bed,cnn,cnr,cns,pdf,png}" - ] - } - - // DEEPVARIANT - withName: 'MERGE_DEEPVARIANT_.*' { - ext.prefix = {"${meta.id}.deepvariant"} - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/deepvariant/${meta.id}/" }, - pattern: "*{vcf.gz,vcf.gz.tbi}" - ] - } - withName: 'MERGE_DEEPVARIANT_GVCF' { - ext.prefix = {"${meta.id}.deepvariant.g"} - } - withName: 'DEEPVARIANT' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.simpleName}" } - ext.args = { params.wes ? "--model_type WES" : "--model_type WGS" } - ext.when = { params.tools && params.tools.split(',').contains('deepvariant') } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/" }, - pattern: "*vcf.gz", - saveAs: { meta.num_intervals > 1 ? null : "deepvariant/${meta.id}/${it}" } - ] - } - withName : 'TABIX_VC_DEEPVARIANT_.*' { - ext.prefix = {"${meta.id}.deepvariant"} - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/deepvariant/${meta.id}/" }, - pattern: "*tbi" - ] - } - - // FREEBAYES - withName: 'MERGE_FREEBAYES' { - ext.prefix = { "${meta.id}.freebayes" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/freebayes/${meta.id}/" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: 'FREEBAYES' { - //To make sure no naming conflicts ensure with module BCFTOOLS_SORT & the naming being correct in the output folder - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}.${target_bed.simpleName}" } - ext.args = '--min-alternate-fraction 0.1 --min-mapping-quality 1' - ext.when = { params.tools && params.tools.split(',').contains('freebayes') } - publishDir = [ - enabled: false - ] - } - - withName: 'BCFTOOLS_SORT' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${vcf.minus("vcf")}.sort" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/" }, - pattern: "*vcf.gz", - saveAs: { meta.num_intervals > 1 ? null : "freebayes/${meta.id}/${it}" } - ] - } - - withName : 'TABIX_VC_FREEBAYES' { - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/freebayes/${meta.id}/" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - // HAPLOTYPECALLER - withName: 'MERGE_HAPLOTYPECALLER' { - ext.prefix = { params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/haplotypecaller/${meta.id}/" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: 'GATK4_HAPLOTYPECALLER' { - ext.args = { params.joint_germline ? "-ERC GVCF" : "" } - ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.simpleName}.g" :"${meta.id}.haplotypecaller.${intervals.simpleName}" ) } - ext.when = { params.tools && params.tools.split(',').contains('haplotypecaller') } - publishDir = [ - enabled: !params.joint_germline, - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/"}, - pattern: "*{vcf.gz,vcf.gz.tbi}", - saveAs: { meta.num_intervals > 1 ? null : "haplotypecaller/${meta.id}/${it}" } - ] - } - - withName: 'CNNSCOREVARIANTS' { - publishDir = [ - // Otherwise it gets published - enabled: false - ] - } - - withName: 'FILTERVARIANTTRANCHES' { - ext.prefix = {"${meta.id}.haplotypecaller"} - ext.args = { "--info-key CNN_1D" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/haplotypecaller/${meta.id}/"}, - pattern: "*{vcf.gz,vcf.gz.tbi}" - ] - } - - withName: 'GATK4_GENOMICSDBIMPORT' { - ext.prefix = { meta.num_intervals > 1 ? "${meta.intervals_name}.joint" : "joint" } - ext.when = { params.tools && params.tools.split(',').contains('haplotypecaller') && params.joint_germline && !params.no_intervals} - } - - withName: 'GATK4_GENOTYPEGVCFS' { - ext.prefix = { meta.num_intervals > 1 ? meta.intervals_name : "joint_germline" } - } - - if (params.tools && params.tools.contains('haplotypecaller') && params.joint_germline){ - withName: 'NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:BCFTOOLS_SORT' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.joint.sort" : "${vcf.minus("vcf.gz")}.sort" } - publishDir = [ - enabled: false - ] - } - } - - withName: 'MERGE_GENOTYPEGVCFS' { - ext.prefix = "joint_germline" - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/haplotypecaller/joint_variant_calling/" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - pattern: "*{vcf.gz,vcf.gz.tbi}" - ] - } - - withName: 'VARIANTRECALIBRATOR_INDEL' { - ext.prefix = { "${meta.id}_INDEL" } - ext.args = "-an QD -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP -mode INDEL" - publishDir = [ - enabled: false - ] - } - - withName: 'VARIANTRECALIBRATOR_SNP' { - ext.prefix = { "${meta.id}_SNP" } - ext.args = "-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP" - publishDir = [ - enabled: false - ] - } - - withName: 'GATK4_APPLYVQSR_SNP' { - ext.prefix = { "${meta.id}_SNP" } - ext.args = '--truth-sensitivity-filter-level 99.9 -mode SNP' - } - - withName: 'GATK4_APPLYVQSR_INDEL' { - ext.prefix = { "${meta.id}_INDEL" } - ext.args = '--truth-sensitivity-filter-level 99.9 -mode INDEL' - } - - withName: 'MERGE_VQSR' { - ext.prefix = "joint_germline_recalibrated" - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/haplotypecaller/joint_variant_calling/"}, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, - pattern: "*{vcf.gz,vcf.gz.tbi}" - ] - } - - // MANTA - withName: 'MERGE_MANTA.*' { - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/manta/${meta.id}/" }, - pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}" - ] - } - withName: 'MERGE_MANTA_DIPLOID' { - ext.prefix = {"${meta.id}.manta.diploid_sv"} - } - withName: 'MERGE_MANTA_SMALL_INDELS' { - ext.prefix = {"${meta.id}.manta.candidate_small_indels"} - } - withName: 'MERGE_MANTA_SV' { - ext.prefix = {"${meta.id}.manta.candidate_sv"} - } - withName: 'MANTA.*' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.manta" : "${meta.id}.manta.${target_bed.simpleName}" } - ext.args = { params.wes ? "--exome" : "" } - ext.when = { params.tools && params.tools.split(',').contains('manta') } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/" }, - pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}", - saveAs: { meta.num_intervals > 1 ? null : "manta/${meta.id}/${it}" } - ] - } - - // STRELKA - withName: 'MERGE_STRELKA.*' { - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/strelka/${meta.id}/" }, - pattern: "*{vcf.gz,vcf.gz.tbi}" - ] - } - withName: 'MERGE_STRELKA' { - ext.prefix = {"${meta.id}.strelka.variants"} - } - withName: 'MERGE_STRELKA_GENOME' { - ext.prefix = {"${meta.id}.strelka.genome"} - } - withName: 'STRELKA_.*' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.strelka" : "${meta.id}.strelka.${target_bed.simpleName}" } - ext.args = { params.wes ? "--exome" : "" } - ext.when = { params.tools && params.tools.split(',').contains('strelka') } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/" }, - pattern: "*{vcf.gz,vcf.gz.tbi}", - saveAs: { meta.num_intervals > 1 ? null : "strelka/${meta.id}/${it}" } - ] - } - - // TIDDIT - withName: 'TIDDIT_SV' { - ext.when = { params.tools && params.tools.split(',').contains('tiddit') } - ext.args = { bwa_index ? "" : "--skip_assembly" } - ext.prefix = { "${meta.id}.tiddit" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" }, - pattern: "*tab", - ] - } - withName : 'TABIX_BGZIP_TIDDIT_SV' { - ext.prefix = { "${meta.id}.tiddit" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" }, - pattern: "*{vcf.gz,vcf.gz.tbi}" - ] - } - -// TUMOR_VARIANT_CALLING - - // CONTROLFREEC - withName: 'ASSESS_SIGNIFICANCE' { - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" }, - pattern: "*{.p.value.txt}" - ] - } - - withName: 'CAT_MPILEUP' { - publishDir = [ - enabled: true, - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/mpileup/${meta.id}/" }, - pattern: "*{mpileup.gz}", - ] - } - - withName: 'FREEC_.*' { - ext.when = { params.tools && params.tools.split(',').contains('controlfreec') } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" }, - pattern: "*{BedGraph,cpn,txt,_CNVs}" - ] - } - - withName: 'FREEC_TUMORONLY' { - ext.args = {[ - "sample":[ - inputformat: 'pileup', - mateorientation: 'FR' - ], - "general" :[ - bedgraphoutput: "TRUE", - breakpointthreshold: params.wes ? "1.2" : "0.8", //Values taken from Freec example configs - breakpointtype: params.wes ? "4" : "2", // Values taken from Freec example configs - coefficientofvariation: params.cf_coeff, - contamination: params.cf_contamination ?: "", - contaminationadjustment: params.cf_contamination_adjustment ? "TRUE" : "", - forcegccontentnormalization: params.wes ? "1" : "0", - minimalsubclonepresence: params.wes ? "30" : "20", - noisydata: params.wes ? "TRUE" : "FALSE", - ploidy: params.cf_ploidy, - printNA: params.wes ? "FALSE" : "TRUE", - readcountthreshold: params.wes ? "50" : "10", - sex: meta.sex, - //uniquematch: not set - window: params.cf_window ?: "" - ], - "BAF":[ - minimalcoverageperposition: params.cf_mincov ?: "", - minimalqualityperposition: params.cf_minqual ?: "", - //"shiftinquality": (optional)not set - ] - ] - } - } - - withName: 'FREEC2BED' { - ext.args = { "${params.cf_ploidy}" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" }, - pattern: "*bed" - ] - } - - withName: 'FREEC2CIRCOS' { - ext.args = { "${params.cf_ploidy}" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" }, - pattern: "*circos.txt" - ] - } - - withName: 'MAKEGRAPH' { - ext.args = { "${params.cf_ploidy}" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" }, - pattern: "*png" - ] - } - - withName: 'SAMTOOLS_MPILEUP' { - ext.when = { params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('mpileup')) } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/mpileup/${meta.id}/" }, - pattern: "*mpileup.gz", - saveAs: { meta.num_intervals > 1 ? null : it } - ] - } - - // MANTA - withName: 'MERGE_MANTA_TUMOR' { - ext.prefix = {"${meta.id}.manta.tumor_sv"} - } - - // MUTECT2 - withName: 'CALCULATECONTAMINATION' { - ext.prefix = { "${meta.id}.mutect2" } - ext.args = { "-tumor-segmentation ${meta.id}.mutect2.segmentation.table" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : "mutect2/${meta.id}/${filename}" } - ] - } - - withName: 'MERGE_MUTECT2.*' { - ext.prefix = { "${meta.id}.mutect2" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/mutect2/${meta.id}" }, - pattern: "*{vcf.gz,vcf.gz.tbi}" - ] - } - - withName: 'FILTERMUTECTCALLS.*' { - ext.prefix = {"${meta.id}.mutect2.filtered"} - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : "mutect2/${meta.id}/${filename}" } - ] - } - - withName: 'GATHERPILEUPSUMMARIES' { - ext.prefix = { "${meta.id}.mutect2" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/mutect2/${meta.id}/" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: 'GATHERPILEUPSUMMARIES_.*' { - ext.prefix = { "${meta.id}.mutect2" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/mutect2/${meta.tumor_id}_vs_${meta.normal_id}/" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: 'GETPILEUPSUMMARIES.*' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/" }, - pattern: "*.table", - saveAs: { meta.num_intervals > 1 ? null : "mutect2/${meta.id}/${it}" } - ] - } - - withName: 'GETPILEUPSUMMARIES_.*' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/" }, - pattern: "*.table", - saveAs: { meta.num_intervals > 1 ? null : "mutect2/${meta.tumor_id}_vs_${meta.normal_id}/${it}" } - ] - } - - withName: 'LEARNREADORIENTATIONMODEL' { - ext.prefix = { "${meta.id}.mutect2.artifactprior" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/mutect2/${meta.id}/" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: 'MERGEMUTECTSTATS' { - ext.prefix = { "${meta.id}.mutect2" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/mutect2/${meta.id}/" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: 'GATK4_MUTECT2' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" } - ext.when = { params.tools && params.tools.split(',').contains('mutect2') } - ext.args = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" : "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/" }, - pattern: "*{vcf.gz,vcf.gz.tbi,stats}", - saveAs: { meta.num_intervals > 1 ? null : "mutect2/${meta.id}/${it}" } - ] - } - -// PAIR_VARIANT_CALLING - - // ASCAT - withName: 'ASCAT' { - - ext.args = {[ - "gender": meta.sex, - "genomeVersion": params.ascat_genome, - "purity": params.ascat_purity, - "ploidy": params.ascat_ploidy, - "minCounts": params.ascat_min_counts, - "chrom_names": meta.sex == 'XX' ? "c(1:22, 'X')" : "c(1:22, 'X', 'Y')", - "min_base_qual": params.ascat_min_base_qual, - "min_map_qual": params.ascat_min_map_qual - ]} - ext.when = { params.tools && params.tools.split(',').contains('ascat') } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/ascat/${meta.id}/" }, - pattern: "*{png,cnvs.txt,metrics.txt,purityploidy.txt,segments.txt,LogR.txt,BAF.txt}" - ] - - } - - // CONTROLFREEC - if (params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('mpileup'))) { - withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_MPILEUP:SAMTOOLS_MPILEUP' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.normal" : "${meta.id}_${intervals.simpleName}.normal" } - } - - withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_MPILEUP:CAT_MPILEUP' { - ext.prefix = { "${meta.id}.normal.mpileup.gz" } - } - - withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_NORMAL:SAMTOOLS_MPILEUP' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.normal" : "${meta.id}_${intervals.simpleName}.normal" } - } - - withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_NORMAL:CAT_MPILEUP' { - ext.prefix = { "${meta.id}.normal.mpileup.gz" } - } - - withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_TUMOR:SAMTOOLS_MPILEUP' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.tumor" : "${meta.id}_${intervals.simpleName}.tumor" } - } - - withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_TUMOR:CAT_MPILEUP' { - ext.prefix = { "${meta.id}.tumor.mpileup.gz" } - } - - withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_MPILEUP:SAMTOOLS_MPILEUP' { - ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.tumor" : "${meta.id}_${intervals.simpleName}.tumor" } - } - - withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_MPILEUP:CAT_MPILEUP' { - ext.prefix = { "${meta.id}.tumor.mpileup.gz" } - } - } - - withName: 'FREEC_SOMATIC' { - ext.args = {[ - "sample":[ - inputformat: 'pileup', - mateorientation: 'FR' - ], - "control":[ - inputformat: "pileup", - mateorientation: "FR" - ], - "general" :[ - bedgraphoutput: "TRUE", - breakpointthreshold: params.wes ? "1.2" : "0.8", //Values taken from Freec example configs - breakpointtype: params.wes ? "4" : "2", // Values taken from Freec example configs - coefficientofvariation: params.cf_coeff, - contamination: params.cf_contamination ?: "", - contaminationadjustment: params.cf_contamination_adjustment ? "TRUE" : "", - forcegccontentnormalization: params.wes ? "1" : "0", - minimalsubclonepresence: params.wes ? "30" : "20", - noisydata: params.wes ? "TRUE" : "FALSE", - ploidy: params.cf_ploidy, - printNA: params.wes ? "FALSE" : "TRUE", - readcountthreshold: params.wes ? "50" : "10", - sex: meta.sex, - //uniquematch: not set - window: params.cf_window ?: "" - ], - "BAF":[ - minimalcoverageperposition: params.cf_mincov ?: "", - minimalqualityperposition: params.cf_minqual ?: "", - //"shiftinquality": (optional)not set - ] - ] - } - } - - // FREEBAYES - if (params.tools && params.tools.split(',').contains('freebayes')) { - withName: '.*:PAIR_VARIANT_CALLING:RUN_FREEBAYES_SOMATIC:FREEBAYES' { - ext.args = "--pooled-continuous \ - --pooled-discrete \ - --genotype-qualities \ - --report-genotype-likelihood-max \ - --allele-balance-priors-off \ - --min-alternate-fraction 0.03 \ - --min-repeat-entropy 1 \ - --min-alternate-count 2 " - } - } - - // MANTA - withName: 'MERGE_MANTA_SOMATIC' { - ext.prefix = {"${meta.id}.manta.somatic_sv"} - } - - // MUTECT2 - if (params.tools && params.tools.split(',').contains('mutect2')) { - withName: 'MUTECT2_PAIRED' { - ext.args = { params.ignore_soft_clipped_bases ? - "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample ${meta.patient}_${meta.normal_id}" : - "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample ${meta.patient}_${meta.normal_id}" } - } - } - - // MSISENSORPRO - withName: 'MSISENSORPRO_MSI_SOMATIC' { - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/msisensorpro/${meta.id}/" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - // STRELKA - withName: 'MERGE_STRELKA_INDELS' { - ext.prefix = {"${meta.id}.strelka.somatic_indels"} - } - withName: 'MERGE_STRELKA_SNVS' { - ext.prefix = {"${meta.id}.strelka.somatic_snvs"} - } - - // TIDDIT - if (params.tools && params.tools.split(',').contains('tiddit')) { - withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TIDDIT:TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' { - ext.prefix = {"${meta.id}.tiddit.normal"} - } - - withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TIDDIT:TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' { - ext.prefix = {"${meta.id}.tiddit.tumor"} - } - - // SVDB - withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TIDDIT:SVDB_MERGE' { - ext.prefix = { "${meta.id}.tiddit" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" }, - pattern: "*vcf.gz" - ] - } - } - - // VCF QC - withName: 'BCFTOOLS_STATS' { - ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('bcftools')) } - ext.prefix = { "${vcf.baseName.minus(".vcf")}" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/reports/bcftools/${meta.variantcaller}/${meta.id}/" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: 'VCFTOOLS_.*' { - ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('vcftools')) } - ext.prefix = { "${variant_file.baseName.minus(".vcf")}" } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/reports/vcftools/${meta.variantcaller}/${meta.id}/" }, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: 'VCFTOOLS_TSTV_COUNT' { - ext.args = "--TsTv-by-count" - } - - withName: 'VCFTOOLS_TSTV_QUAL' { - ext.args = "--TsTv-by-qual" - } - - withName: 'VCFTOOLS_SUMMARY' { - ext.args = "--FILTER-summary" - } - -// ANNOTATE - - // SNPEFF - if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) { - withName: 'SNPEFF' { - ext.prefix = { "${vcf.baseName.minus(".vcf")}_snpEff" } - ext.args = '-nodownload -canon -v' - if (!params.snpeff_cache) container = { params.snpeff_genome ? "nfcore/snpeff:${params.snpeff_version}.${params.snpeff_genome}" : "nfcore/snpeff:${params.snpeff_version}.${params.genome}" } - publishDir = [ - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/reports/snpeff/${meta.variantcaller}/${meta.id}/" }, - pattern: "*{csv,html,genes.txt}", - saveAs: { params.tools.split(',').contains('snpeff') ? it : null } - ] - ] - } - } - - // VEP - if (params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) { - withName: 'ENSEMBLVEP' { - ext.args = { [ - '--everything --filter_common --per_gene --total_length --offline --format vcf', - (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', - (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', - (params.vep_loftee) ? "--plugin LoF,loftee_path:/opt/conda/envs/nf-core-vep-${params.vep_version}/share/ensembl-vep-${params.vep_version}-0" : '', - (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '', - (params.vep_spliceregion) ? '--plugin SpliceRegion' : '', - (params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf' - ].join(' ').trim() } - // If just VEP: _VEP.ann.vcf - ext.prefix = { "${vcf.baseName.minus(".vcf")}_VEP" } - if (!params.vep_cache) container = { params.vep_genome ? "nfcore/vep:${params.vep_version}.${params.vep_genome}" : "nfcore/vep:${params.vep_version}.${params.genome}" } - publishDir = [ - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/reports/EnsemblVEP/${meta.variantcaller}/${meta.id}/" }, - pattern: "*html" - ], - [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, - pattern: "*{json,tab}" - ] - ] - } - } - - // SNPEFF THEN VEP - if (params.tools && params.tools.split(',').contains('merge')) { - withName: "NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP" { - // If merge: Output file will have format *_snpEff_VEP.ann.vcf, *_snpEff_VEP.ann.json or *_snpEff_VEP.ann.tab - ext.prefix = { "${vcf.baseName.minus(".ann.vcf")}_VEP" } - } - } - - // ALL ANNOTATION TOOLS - if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) { - withName: "NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:.*:TABIX_BGZIPTABIX" { - ext.prefix = { input.baseName.minus(".vcf") } - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, - pattern: "*{gz,gz.tbi}" - ] - } - } - - if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) { - withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX' { - publishDir = [ - mode: params.publish_dir_mode, - path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, - pattern: "*{gz,gz.tbi}", - saveAs: { params.tools.split(',').contains('snpeff') ? it : null } - ] - } - } -} diff --git a/conf/modules/aligner.config b/conf/modules/aligner.config new file mode 100644 index 0000000000..68e1cfdd28 --- /dev/null +++ b/conf/modules/aligner.config @@ -0,0 +1,66 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// MAPPING + +process { + + if (params.step == 'mapping') { + withName: "BWAMEM1_MEM" { + ext.when = { params.aligner == "bwa-mem" } + } + + withName: "BWAMEM2_MEM" { + ext.when = { params.aligner == "bwa-mem2" } + } + + withName: "DRAGMAP_ALIGN" { + ext.when = { params.aligner == "dragmap" } + ext.args = { "--RGSM ${meta.read_group}" } + } + + withName: "(BWAMEM.*_MEM|DRAGMAP_ALIGN)" { + // Markduplicates Spark NEEDS name-sorted reads or runtime goes through the roof + // However if it's skipped, reads need to be coordinate-sorted + // Only name sort if Spark for Markduplicates + duplicate marking is not skipped + ext.args2 = { params.use_gatk_spark && params.use_gatk_spark.contains('markduplicates') && (!params.skip_tools || (params.skip_tools && !params.skip_tools.split(',').contains('markduplicates'))) ? '-n' : '' } + ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "${meta.id}.sorted" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/preprocessing/" }, + pattern: "*bam", + // Only save if (save_mapped OR (no_markduplicates AND save_output_as_bam)) AND only a single BAM file per sample + saveAs: { (params.save_output_as_bam && (params.save_mapped || params.skip_tools && params.skip_tools.split(',').contains('markduplicates'))) && (meta.size * meta.numLanes == 1) ? "mapped/${meta.id}/${it}" : null } + ] + } + + withName: "BWAMEM.*_MEM" { + // Using -B 3 for tumor samples + ext.args = { meta.status == 1 ? "-K 100000000 -Y -B 3 -R ${meta.read_group}" : "-K 100000000 -Y -R ${meta.read_group}" } + } + } + + withName: 'MERGE_BAM|INDEX_MERGE_BAM' { + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/preprocessing/" }, + pattern: "*{bam,bai}", + // Only save if (save_output_as_bam AND (no_markduplicates OR save_mapped )) + saveAs: { (params.save_output_as_bam && (params.save_mapped || params.skip_tools && params.skip_tools.split(',').contains('markduplicates'))) ? "mapped/${meta.id}/${it}" : null } + ] + } + + withName: 'MERGE_BAM' { + ext.prefix = { "${meta.id}.sorted" } + } +} diff --git a/conf/modules/alignment_to_fastq.config b/conf/modules/alignment_to_fastq.config new file mode 100644 index 0000000000..b207e57740 --- /dev/null +++ b/conf/modules/alignment_to_fastq.config @@ -0,0 +1,85 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// BAM TO FASTQ + +process { + + withName: 'COLLATE_FASTQ_MAP' { + ext.args2 = '-N' + ext.prefix = {"${meta.id}.mapped"} + publishDir = [ + //specify to avoid publishing, overwritten otherwise + enabled: false + ] + } + + withName: 'COLLATE_FASTQ_UNMAP' { + ext.args2 = '-N' + ext.prefix = {"${meta.id}.unmapped"} + publishDir = [ + //specify to avoid publishing, overwritten otherwise + enabled: false + ] + } + + withName: 'SAMTOOLS_VIEW_MAP_MAP' { + ext.args = '-b -f1 -F12' + ext.prefix = {"${meta.id}.map_map"} + publishDir = [ + //specify to avoid publishing, overwritten otherwise + enabled: false + ] + } + + withName: 'SAMTOOLS_VIEW_MAP_UNMAP' { + ext.args = '-b -f8 -F260' + ext.prefix = {"${meta.id}.map_unmap"} + publishDir = [ + //specify to avoid publishing, overwritten otherwise + enabled: false + ] + } + + withName: 'SAMTOOLS_VIEW_UNMAP_MAP' { + ext.args = '-b -f4 -F264' + ext.prefix = {"${meta.id}.unmap_map"} + publishDir = [ + //specify to avoid publishing, overwritten otherwise + enabled: false + ] + } + + withName: 'SAMTOOLS_VIEW_UNMAP_UNMAP' { + ext.args = '-b -f12 -F256' + ext.prefix = {"${meta.id}.unmap_unmap"} + publishDir = [ + //specify to avoid publishing, overwritten otherwise + enabled: false + ] + } + + withName: 'SAMTOOLS_MERGE_UNMAP' { + ext.prefix = {"${meta.id}.merged_unmap"} + publishDir = [ + //specify to avoid publishing, overwritten otherwise + enabled: false + ] + } + withName: 'CAT_FASTQ' { + publishDir = [ + //specify to avoid publishing, overwritten otherwise + enabled: false + ] + } +} diff --git a/conf/modules/annotate.config b/conf/modules/annotate.config new file mode 100644 index 0000000000..7d0b1eb523 --- /dev/null +++ b/conf/modules/annotate.config @@ -0,0 +1,95 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// ANNOTATE + +process { + + // SNPEFF + if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) { + withName: 'SNPEFF' { + ext.prefix = { "${vcf.baseName.minus(".vcf")}_snpEff" } + ext.args = '-nodownload -canon -v' + if (!params.snpeff_cache) container = { params.snpeff_genome ? "nfcore/snpeff:${params.snpeff_version}.${params.snpeff_genome}" : "nfcore/snpeff:${params.snpeff_version}.${params.genome}" } + publishDir = [ + [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/reports/snpeff/${meta.variantcaller}/${meta.id}/" }, + pattern: "*{csv,html,genes.txt}", + saveAs: { params.tools.split(',').contains('snpeff') ? it : null } + ] + ] + } + } + + // VEP + if (params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) { + withName: 'ENSEMBLVEP' { + ext.args = { [ + '--everything --filter_common --per_gene --total_length --offline --format vcf', + (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence) ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', + (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence) ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}" : '', + (params.vep_loftee) ? "--plugin LoF,loftee_path:/opt/conda/envs/nf-core-vep-${params.vep_version}/share/ensembl-vep-${params.vep_version}-0" : '', + (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}" : '', + (params.vep_spliceregion) ? '--plugin SpliceRegion' : '', + (params.vep_out_format) ? "--${params.vep_out_format}" : '--vcf' + ].join(' ').trim() } + // If just VEP: _VEP.ann.vcf + ext.prefix = { "${vcf.baseName.minus(".vcf")}_VEP" } + if (!params.vep_cache) container = { params.vep_genome ? "nfcore/vep:${params.vep_version}.${params.vep_genome}" : "nfcore/vep:${params.vep_version}.${params.genome}" } + publishDir = [ + [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/reports/EnsemblVEP/${meta.variantcaller}/${meta.id}/" }, + pattern: "*html" + ], + [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, + pattern: "*{json,tab}" + ] + ] + } + } + + // SNPEFF THEN VEP + if (params.tools && params.tools.split(',').contains('merge')) { + withName: "NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_MERGE:ENSEMBLVEP" { + // If merge: Output file will have format *_snpEff_VEP.ann.vcf, *_snpEff_VEP.ann.json or *_snpEff_VEP.ann.tab + ext.prefix = { "${vcf.baseName.minus(".ann.vcf")}_VEP" } + } + } + + // ALL ANNOTATION TOOLS + if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) { + withName: "NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:.*:TABIX_BGZIPTABIX" { + ext.prefix = { input.baseName.minus(".vcf") } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, + pattern: "*{gz,gz.tbi}" + ] + } + } + + if (params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge'))) { + withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX' { + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" }, + pattern: "*{gz,gz.tbi}", + saveAs: { params.tools.split(',').contains('snpeff') ? it : null } + ] + } + } +} diff --git a/conf/modules/ascat.config b/conf/modules/ascat.config new file mode 100644 index 0000000000..9ee66663a0 --- /dev/null +++ b/conf/modules/ascat.config @@ -0,0 +1,36 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// ASCAT + +process { + + withName: 'ASCAT' { + ext.args = {[ + "gender": meta.sex, + "genomeVersion": params.ascat_genome, + "purity": params.ascat_purity, + "ploidy": params.ascat_ploidy, + "minCounts": params.ascat_min_counts, + "chrom_names": meta.sex == 'XX' ? "c(1:22, 'X')" : "c(1:22, 'X', 'Y')", + "min_base_qual": params.ascat_min_base_qual, + "min_map_qual": params.ascat_min_map_qual + ]} + ext.when = { params.tools && params.tools.split(',').contains('ascat') } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/ascat/${meta.id}/" }, + pattern: "*{png,cnvs.txt,metrics.txt,purityploidy.txt,segments.txt,LogR.txt,BAF.txt}" + ] + } +} diff --git a/conf/modules/cnvkit.config b/conf/modules/cnvkit.config new file mode 100644 index 0000000000..93b06518b5 --- /dev/null +++ b/conf/modules/cnvkit.config @@ -0,0 +1,50 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// CNVKIT + +process { + +// PREPARE REFERENCE CNVKIT + withName: 'CNVKIT_ANTITARGET' { + ext.when = { params.tools && params.tools.split(',').contains('cnvkit') } + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference/cnvkit" }, + pattern: "*{bed}" + ] + } + + withName: 'CNVKIT_REFERENCE' { + ext.prefix = "cnvkit" + ext.when = { params.tools && params.tools.split(',').contains('cnvkit') } + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference/cnvkit" }, + pattern: "*{cnn}" + ] + } + + // CNVKIT + withName: 'CNVKIT_BATCH' { + ext.args = { params.wes ? "--method hybrid --diagram --scatter" : "--method wgs --diagram --scatter" } + ext.when = { params.tools && params.tools.split(',').contains('cnvkit') } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/cnvkit/${meta.id}/" }, + pattern: "*{bed,cnn,cnr,cns,pdf,png}" + ] + } +} diff --git a/conf/modules/controlfreec.config b/conf/modules/controlfreec.config new file mode 100644 index 0000000000..3945756957 --- /dev/null +++ b/conf/modules/controlfreec.config @@ -0,0 +1,131 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// CONTROLFREEC + +process { + + withName: 'ASSESS_SIGNIFICANCE' { + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" }, + pattern: "*{.p.value.txt}" + ] + } + + withName: 'FREEC_.*' { + ext.when = { params.tools && params.tools.split(',').contains('controlfreec') } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" }, + pattern: "*{BedGraph,cpn,txt,_CNVs}" + ] + } + + withName: 'FREEC2BED' { + ext.args = { "${params.cf_ploidy}" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" }, + pattern: "*bed" + ] + } + + withName: 'FREEC2CIRCOS' { + ext.args = { "${params.cf_ploidy}" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" }, + pattern: "*circos.txt" + ] + } + + withName: 'MAKEGRAPH' { + ext.args = { "${params.cf_ploidy}" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/controlfreec/${meta.id}/" }, + pattern: "*png" + ] + } + +// TUMOR_ONLY_VARIANT_CALLING + withName: 'FREEC_TUMORONLY' { + ext.args = {[ + "sample":[ + inputformat: 'pileup', + mateorientation: 'FR' + ], + "general" :[ + bedgraphoutput: "TRUE", + breakpointthreshold: params.wes ? "1.2" : "0.8", //Values taken from Freec example configs + breakpointtype: params.wes ? "4" : "2", // Values taken from Freec example configs + coefficientofvariation: params.cf_coeff, + contamination: params.cf_contamination ?: "", + contaminationadjustment: params.cf_contamination_adjustment ? "TRUE" : "", + forcegccontentnormalization: params.wes ? "1" : "0", + minimalsubclonepresence: params.wes ? "30" : "20", + noisydata: params.wes ? "TRUE" : "FALSE", + ploidy: params.cf_ploidy, + printNA: params.wes ? "FALSE" : "TRUE", + readcountthreshold: params.wes ? "50" : "10", + sex: meta.sex, + //uniquematch: not set + window: params.cf_window ?: "" + ], + "BAF":[ + minimalcoverageperposition: params.cf_mincov ?: "", + minimalqualityperposition: params.cf_minqual ?: "", + //"shiftinquality": (optional)not set + ] + ] + } + } + +// PAIR_VARIANT_CALLING + withName: 'FREEC_SOMATIC' { + ext.args = {[ + "sample":[ + inputformat: 'pileup', + mateorientation: 'FR' + ], + "control":[ + inputformat: "pileup", + mateorientation: "FR" + ], + "general" :[ + bedgraphoutput: "TRUE", + breakpointthreshold: params.wes ? "1.2" : "0.8", //Values taken from Freec example configs + breakpointtype: params.wes ? "4" : "2", // Values taken from Freec example configs + coefficientofvariation: params.cf_coeff, + contamination: params.cf_contamination ?: "", + contaminationadjustment: params.cf_contamination_adjustment ? "TRUE" : "", + forcegccontentnormalization: params.wes ? "1" : "0", + minimalsubclonepresence: params.wes ? "30" : "20", + noisydata: params.wes ? "TRUE" : "FALSE", + ploidy: params.cf_ploidy, + printNA: params.wes ? "FALSE" : "TRUE", + readcountthreshold: params.wes ? "50" : "10", + sex: meta.sex, + //uniquematch: not set + window: params.cf_window ?: "" + ], + "BAF":[ + minimalcoverageperposition: params.cf_mincov ?: "", + minimalqualityperposition: params.cf_minqual ?: "", + //"shiftinquality": (optional)not set + ] + ] + } + } +} diff --git a/conf/modules/deepvariant.config b/conf/modules/deepvariant.config new file mode 100644 index 0000000000..f91e792447 --- /dev/null +++ b/conf/modules/deepvariant.config @@ -0,0 +1,51 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// DEEPVARIANT + +process { + + withName: 'DEEPVARIANT' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.deepvariant" : "${meta.id}.deepvariant.${intervals.simpleName}" } + ext.args = { params.wes ? "--model_type WES" : "--model_type WGS" } + ext.when = { params.tools && params.tools.split(',').contains('deepvariant') } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/" }, + pattern: "*vcf.gz", + saveAs: { meta.num_intervals > 1 ? null : "deepvariant/${meta.id}/${it}" } + ] + } + + withName: 'MERGE_DEEPVARIANT_.*' { + ext.prefix = {"${meta.id}.deepvariant"} + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/deepvariant/${meta.id}/" }, + pattern: "*{vcf.gz,vcf.gz.tbi}" + ] + } + + withName: 'MERGE_DEEPVARIANT_GVCF' { + ext.prefix = {"${meta.id}.deepvariant.g"} + } + + withName : 'TABIX_VC_DEEPVARIANT_.*' { + ext.prefix = {"${meta.id}.deepvariant"} + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/deepvariant/${meta.id}/" }, + pattern: "*tbi" + ] + } +} diff --git a/conf/modules/freebayes.config b/conf/modules/freebayes.config new file mode 100644 index 0000000000..a36193ec09 --- /dev/null +++ b/conf/modules/freebayes.config @@ -0,0 +1,68 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// FREEBAYES + +process { + + withName: 'MERGE_FREEBAYES' { + ext.prefix = { "${meta.id}.freebayes" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/freebayes/${meta.id}/" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'FREEBAYES' { + ext.args = '--min-alternate-fraction 0.1 --min-mapping-quality 1' + //To make sure no naming conflicts ensure with module BCFTOOLS_SORT & the naming being correct in the output folder + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}" : "${meta.id}.${target_bed.simpleName}" } + ext.when = { params.tools && params.tools.split(',').contains('freebayes') } + publishDir = [ + enabled: false + ] + } + + withName: 'BCFTOOLS_SORT' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.freebayes" : "${vcf.minus("vcf")}.sort" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/" }, + pattern: "*vcf.gz", + saveAs: { meta.num_intervals > 1 ? null : "freebayes/${meta.id}/${it}" } + ] + } + + withName : 'TABIX_VC_FREEBAYES' { + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/freebayes/${meta.id}/" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + // PAIR_VARIANT_CALLING + if (params.tools && params.tools.split(',').contains('freebayes')) { + withName: '.*:PAIR_VARIANT_CALLING:RUN_FREEBAYES_SOMATIC:FREEBAYES' { + ext.args = "--pooled-continuous \ + --pooled-discrete \ + --genotype-qualities \ + --report-genotype-likelihood-max \ + --allele-balance-priors-off \ + --min-alternate-fraction 0.03 \ + --min-repeat-entropy 1 \ + --min-alternate-count 2 " + } + } +} diff --git a/conf/modules/haplotypecaller.config b/conf/modules/haplotypecaller.config new file mode 100644 index 0000000000..53c3a7e5b8 --- /dev/null +++ b/conf/modules/haplotypecaller.config @@ -0,0 +1,120 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// HAPLOTYPECALLER + +process { + + withName: 'GATK4_HAPLOTYPECALLER' { + ext.args = { params.joint_germline ? "-ERC GVCF" : "" } + ext.prefix = { meta.num_intervals <= 1 ? ( params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" ) : ( params.joint_germline ? "${meta.id}.haplotypecaller.${intervals.simpleName}.g" :"${meta.id}.haplotypecaller.${intervals.simpleName}" ) } + ext.when = { params.tools && params.tools.split(',').contains('haplotypecaller') } + publishDir = [ + enabled: !params.joint_germline, + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/"}, + pattern: "*{vcf.gz,vcf.gz.tbi}", + saveAs: { meta.num_intervals > 1 ? null : "haplotypecaller/${meta.id}/${it}" } + ] + } + + withName: 'MERGE_HAPLOTYPECALLER' { + ext.prefix = { params.joint_germline ? "${meta.id}.haplotypecaller.g" : "${meta.id}.haplotypecaller" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/haplotypecaller/${meta.id}/" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'CNNSCOREVARIANTS' { + publishDir = [ + // Otherwise it gets published + enabled: false + ] + } + + withName: 'FILTERVARIANTTRANCHES' { + ext.prefix = {"${meta.id}.haplotypecaller"} + ext.args = { "--info-key CNN_1D" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/haplotypecaller/${meta.id}/"}, + pattern: "*{vcf.gz,vcf.gz.tbi}" + ] + } + + withName: 'GATK4_GENOMICSDBIMPORT' { + ext.prefix = { meta.num_intervals > 1 ? "${meta.intervals_name}.joint" : "joint" } + ext.when = { params.tools && params.tools.split(',').contains('haplotypecaller') && params.joint_germline && !params.no_intervals} + } + + withName: 'GATK4_GENOTYPEGVCFS' { + ext.prefix = { meta.num_intervals > 1 ? meta.intervals_name : "joint_germline" } + } + + if (params.tools && params.tools.contains('haplotypecaller') && params.joint_germline){ + withName: 'NFCORE_SAREK:SAREK:GERMLINE_VARIANT_CALLING:RUN_HAPLOTYPECALLER:JOINT_GERMLINE:BCFTOOLS_SORT' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.joint.sort" : "${vcf.minus("vcf.gz")}.sort" } + publishDir = [ + enabled: false + ] + } + } + + withName: 'MERGE_GENOTYPEGVCFS' { + ext.prefix = "joint_germline" + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/haplotypecaller/joint_variant_calling/" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + pattern: "*{vcf.gz,vcf.gz.tbi}" + ] + } + + withName: 'VARIANTRECALIBRATOR_INDEL' { + ext.prefix = { "${meta.id}_INDEL" } + ext.args = "-an QD -an MQRankSum -an ReadPosRankSum -an FS -an SOR -an DP -mode INDEL" + publishDir = [ + enabled: false + ] + } + + withName: 'VARIANTRECALIBRATOR_SNP' { + ext.prefix = { "${meta.id}_SNP" } + ext.args = "-an QD -an MQ -an MQRankSum -an ReadPosRankSum -an FS -an SOR -mode SNP" + publishDir = [ + enabled: false + ] + } + + withName: 'GATK4_APPLYVQSR_SNP' { + ext.prefix = { "${meta.id}_SNP" } + ext.args = '--truth-sensitivity-filter-level 99.9 -mode SNP' + } + + withName: 'GATK4_APPLYVQSR_INDEL' { + ext.prefix = { "${meta.id}_INDEL" } + ext.args = '--truth-sensitivity-filter-level 99.9 -mode INDEL' + } + + withName: 'MERGE_VQSR' { + ext.prefix = "joint_germline_recalibrated" + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/haplotypecaller/joint_variant_calling/"}, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + pattern: "*{vcf.gz,vcf.gz.tbi}" + ] + } +} diff --git a/conf/modules/manta.config b/conf/modules/manta.config new file mode 100644 index 0000000000..944025af07 --- /dev/null +++ b/conf/modules/manta.config @@ -0,0 +1,57 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// MANTA + +process { + + withName: 'MANTA.*' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.manta" : "${meta.id}.manta.${target_bed.simpleName}" } + ext.args = { params.wes ? "--exome" : "" } + ext.when = { params.tools && params.tools.split(',').contains('manta') } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/" }, + pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}", + saveAs: { meta.num_intervals > 1 ? null : "manta/${meta.id}/${it}" } + ] + } + + withName: 'MERGE_MANTA.*' { + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/manta/${meta.id}/" }, + pattern: "*{diploid_sv,tumor_sv,somatic_sv}.{vcf.gz,vcf.gz.tbi}" + ] + } + + withName: 'MERGE_MANTA_DIPLOID' { + ext.prefix = {"${meta.id}.manta.diploid_sv"} + } + + withName: 'MERGE_MANTA_SMALL_INDELS' { + ext.prefix = {"${meta.id}.manta.candidate_small_indels"} + } + + withName: 'MERGE_MANTA_SV' { + ext.prefix = {"${meta.id}.manta.candidate_sv"} + } + + withName: 'MERGE_MANTA_TUMOR' { + ext.prefix = {"${meta.id}.manta.tumor_sv"} + } + + withName: 'MERGE_MANTA_SOMATIC' { + ext.prefix = {"${meta.id}.manta.somatic_sv"} + } +} diff --git a/conf/modules/markduplicates.config b/conf/modules/markduplicates.config new file mode 100644 index 0000000000..08bfd85688 --- /dev/null +++ b/conf/modules/markduplicates.config @@ -0,0 +1,110 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// MARKDUPLICATES + +process { + + withName: 'CRAM_TO_BAM' { + ext.args = "-b" + } + + withName: 'BAM_TO_CRAM' { + // BAM provided for step Markduplicates either run through MD or Convert -> then saved as sorted.cram (convert) or md.cram (md directly) + // BAM files provided for step prepare_recal are converted and run through BQSR -> then saved as md.cram + // BAM files provided for step recal are converted and run through BQSR II -> then saved as md.cram + ext.args = "-C" + ext.prefix = { "${meta.id}.converted" } + publishDir = [ + enabled: !params.save_output_as_bam, + mode: params.publish_dir_mode, + path: { "${params.outdir}/preprocessing/converted/${meta.id}" }, + pattern: "*{cram,crai}" + ] + } + + withName: 'BAM_TO_CRAM_MAPPING' { + // Run only when mapping should be saved as CRAM or when no MD is done + ext.when = (params.save_mapped && !params.save_output_as_bam) || (params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) + ext.prefix = { "${meta.id}.sorted" } + publishDir = [ + // Never publish if BAM only should be published + enabled: !params.save_output_as_bam, + mode: params.publish_dir_mode, + path: { "${params.outdir}/preprocessing/mapped/${meta.id}/" }, + pattern: "*{cram,crai}" + ] + } + + withName: 'GATK4_ESTIMATELIBRARYCOMPLEXITY' { + ext.prefix = { "${meta.id}.md.cram" } + ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates_report')) } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/reports/markduplicates/${meta.id}" }, + pattern: "*metrics" + ] + } + + withName: 'GATK4_MARKDUPLICATES' { + ext.args = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true' + ext.prefix = { "${meta.id}.md.cram" } + ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) } + publishDir = [ + [ + enabled: !params.save_output_as_bam, + mode: params.publish_dir_mode, + path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" }, + pattern: "*{cram,crai}" + ], + [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/reports/" }, + pattern: "*metrics", + saveAs: { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates_report')) ? "markduplicates/${meta.id}/${it}" : null} + ] + ] + } + + withName: 'GATK4_MARKDUPLICATES_SPARK' { + ext.args = '--remove-sequencing-duplicates false -VS LENIENT' + ext.prefix = { "${meta.id}.md.cram" } + publishDir = [ + enabled: !params.save_output_as_bam, + mode: params.publish_dir_mode, + path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" }, + pattern: "*{cram,crai}" + ] + } + + withName: 'INDEX_MARKDUPLICATES' { + publishDir = [ + enabled: !params.save_output_as_bam, + mode: params.publish_dir_mode, + path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" }, + pattern: "*{cram,crai}" + ] + } + + + withName: 'NFCORE_SAREK:SAREK:CRAM_TO_BAM' { + ext.prefix = { "${meta.id}.md" } + ext.when = { params.save_output_as_bam } + publishDir = [ + enabled: params.save_output_as_bam, + mode: params.publish_dir_mode, + path: { "${params.outdir}/preprocessing/markduplicates/${meta.id}/" }, + pattern: "*{md.bam,md.bam.bai}" + ] + } +} diff --git a/conf/modules/modules.config b/conf/modules/modules.config new file mode 100644 index 0000000000..0c36169370 --- /dev/null +++ b/conf/modules/modules.config @@ -0,0 +1,122 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +process { + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + + withName: CUSTOM_DUMPSOFTWAREVERSIONS { + cache = false + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/pipeline_info" }, + pattern: '*_versions.yml' + ] + } + +// QC + withName: 'FASTQC' { + ext.args = '--quiet' + ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('fastqc')) } + publishDir = [ + [ + path: { "${params.outdir}/reports/fastqc/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{html,zip}" + ] + ] + } + + withName: 'NFCORE_SAREK:SAREK:(BAM_MARKDUPLICATES|BAM_MARKDUPLICATES_SPARK):CRAM_QC_MOSDEPTH_SAMTOOLS:SAMTOOLS_STATS' { + ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) } + ext.prefix = { "${meta.id}.md.cram" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/reports/samtools/${meta.id}" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS' { + ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) } + ext.prefix = { "${meta.id}.sorted.cram" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/reports/samtools/${meta.id}" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'MOSDEPTH' { + ext.args = { !params.wes ? "-n --fast-mode --by 500" : ""} + ext.prefix = { params.skip_tools && params.skip_tools.split(',').contains('markduplicates') ? "${meta.id}.sorted" : "${meta.id}.md" } + ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('mosdepth')) } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/reports/mosdepth/${meta.id}" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, + ] + } + + if ((params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') && (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator')))) { + withName: 'NFCORE_SAREK:SAREK:CRAM_QC_RECAL:MOSDEPTH' { + ext.prefix = { "${meta.id}.recal" } + } + + withName: 'NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS' { + ext.prefix = { "${meta.id}.recal.cram" } + ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('samtools')) } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/reports/samtools/${meta.id}" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + } + + // VCF + withName: 'BCFTOOLS_STATS' { + ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('bcftools')) } + ext.prefix = { "${vcf.baseName.minus(".vcf")}" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/reports/bcftools/${meta.variantcaller}/${meta.id}/" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'VCFTOOLS_.*' { + ext.when = { !(params.skip_tools && params.skip_tools.split(',').contains('vcftools')) } + ext.prefix = { "${variant_file.baseName.minus(".vcf")}" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/reports/vcftools/${meta.variantcaller}/${meta.id}/" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'VCFTOOLS_TSTV_COUNT' { + ext.args = "--TsTv-by-count" + } + + withName: 'VCFTOOLS_TSTV_QUAL' { + ext.args = "--TsTv-by-qual" + } + + withName: 'VCFTOOLS_SUMMARY' { + ext.args = "--FILTER-summary" + } +} diff --git a/conf/modules/mpileup.config b/conf/modules/mpileup.config new file mode 100644 index 0000000000..8c48d9b359 --- /dev/null +++ b/conf/modules/mpileup.config @@ -0,0 +1,71 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// MPILEUP + +process { + + withName: 'CAT_MPILEUP' { + publishDir = [ + enabled: true, + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/mpileup/${meta.id}/" }, + pattern: "*{mpileup.gz}", + ] + } + + withName: 'SAMTOOLS_MPILEUP' { + ext.when = { params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('mpileup')) } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/mpileup/${meta.id}/" }, + pattern: "*mpileup.gz", + saveAs: { meta.num_intervals > 1 ? null : it } + ] + } + +// PAIR_VARIANT_CALLING + if (params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('mpileup'))) { + withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_MPILEUP:SAMTOOLS_MPILEUP' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.normal" : "${meta.id}_${intervals.simpleName}.normal" } + } + + withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_MPILEUP:CAT_MPILEUP' { + ext.prefix = { "${meta.id}.normal.mpileup.gz" } + } + + withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_NORMAL:SAMTOOLS_MPILEUP' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.normal" : "${meta.id}_${intervals.simpleName}.normal" } + } + + withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_NORMAL:CAT_MPILEUP' { + ext.prefix = { "${meta.id}.normal.mpileup.gz" } + } + + withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_TUMOR:SAMTOOLS_MPILEUP' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.tumor" : "${meta.id}_${intervals.simpleName}.tumor" } + } + + withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:MPILEUP_TUMOR:CAT_MPILEUP' { + ext.prefix = { "${meta.id}.tumor.mpileup.gz" } + } + + withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_MPILEUP:SAMTOOLS_MPILEUP' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.tumor" : "${meta.id}_${intervals.simpleName}.tumor" } + } + + withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_TUMOR_ONLY_ALL:BAM_VARIANT_CALLING_MPILEUP:CAT_MPILEUP' { + ext.prefix = { "${meta.id}.tumor.mpileup.gz" } + } + } +} diff --git a/conf/modules/msisensorpro.config b/conf/modules/msisensorpro.config new file mode 100644 index 0000000000..574068e6b4 --- /dev/null +++ b/conf/modules/msisensorpro.config @@ -0,0 +1,25 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// MSISENSORPRO + +process { + + withName: 'MSISENSORPRO_MSI_SOMATIC' { + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/msisensorpro/${meta.id}/" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} diff --git a/conf/modules/mutect2.config b/conf/modules/mutect2.config new file mode 100644 index 0000000000..63572f7931 --- /dev/null +++ b/conf/modules/mutect2.config @@ -0,0 +1,123 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// MUTECT2 + +process { + +// TUMOR_ONLY_VARIANT_CALLING + withName: 'CALCULATECONTAMINATION' { + ext.prefix = { "${meta.id}.mutect2" } + ext.args = { "-tumor-segmentation ${meta.id}.mutect2.segmentation.table" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : "mutect2/${meta.id}/${filename}" } + ] + } + + withName: 'MERGE_MUTECT2.*' { + ext.prefix = { "${meta.id}.mutect2" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/mutect2/${meta.id}" }, + pattern: "*{vcf.gz,vcf.gz.tbi}" + ] + } + + withName: 'FILTERMUTECTCALLS.*' { + ext.prefix = {"${meta.id}.mutect2.filtered"} + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : "mutect2/${meta.id}/${filename}" } + ] + } + + withName: 'GATHERPILEUPSUMMARIES' { + ext.prefix = { "${meta.id}.mutect2" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/mutect2/${meta.id}/" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'GATHERPILEUPSUMMARIES_.*' { + ext.prefix = { "${meta.id}.mutect2" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/mutect2/${meta.tumor_id}_vs_${meta.normal_id}/" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'GETPILEUPSUMMARIES.*' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/" }, + pattern: "*.table", + saveAs: { meta.num_intervals > 1 ? null : "mutect2/${meta.id}/${it}" } + ] + } + + withName: 'GETPILEUPSUMMARIES_.*' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/" }, + pattern: "*.table", + saveAs: { meta.num_intervals > 1 ? null : "mutect2/${meta.tumor_id}_vs_${meta.normal_id}/${it}" } + ] + } + + withName: 'LEARNREADORIENTATIONMODEL' { + ext.prefix = { "${meta.id}.mutect2.artifactprior" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/mutect2/${meta.id}/" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'MERGEMUTECTSTATS' { + ext.prefix = { "${meta.id}.mutect2" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/mutect2/${meta.id}/" }, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + + withName: 'GATK4_MUTECT2' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" } + ext.when = { params.tools && params.tools.split(',').contains('mutect2') } + ext.args = { params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" : "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/" }, + pattern: "*{vcf.gz,vcf.gz.tbi,stats}", + saveAs: { meta.num_intervals > 1 ? null : "mutect2/${meta.id}/${it}" } + ] + } + +// PAIR_VARIANT_CALLING + if (params.tools && params.tools.split(',').contains('mutect2')) { + withName: 'MUTECT2_PAIRED' { + ext.args = { params.ignore_soft_clipped_bases ? + "--dont-use-soft-clipped-bases true --f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample ${meta.patient}_${meta.normal_id}" : + "--f1r2-tar-gz ${task.ext.prefix}.f1r2.tar.gz --normal-sample ${meta.patient}_${meta.normal_id}" } + } + } +} diff --git a/conf/modules/prepare_genome.config b/conf/modules/prepare_genome.config new file mode 100644 index 0000000000..dbb88dd3d8 --- /dev/null +++ b/conf/modules/prepare_genome.config @@ -0,0 +1,138 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// PREPARE_GENOME + +process { + + withName: 'BWAMEM1_INDEX' { + ext.when = { !params.bwa && params.step == "mapping" && params.aligner == "bwa-mem" } + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference" }, + pattern: "bwa" + ] + } + + withName: 'BWAMEM2_INDEX' { + ext.when = { !params.bwamem2 && params.step == "mapping" && params.aligner == "bwa-mem2" } + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference" }, + pattern: "bwamem2" + ] + } + + withName: 'DRAGMAP_HASHTABLE' { + ext.when = { !params.dragmap && params.step == "mapping" && params.aligner == "dragmap" } + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference" }, + pattern: "dragmap" + ] + } + + withName: 'GATK4_CREATESEQUENCEDICTIONARY' { + ext.when = { !params.dict && params.step != "annotate" && params.step != "controlfreec" } + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference/dict" }, + pattern: "*dict" + ] + } + + withName: 'MSISENSORPRO_SCAN' { + ext.when = { params.tools && params.tools.split(',').contains('msisensorpro') } + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference/msi" }, + pattern: "*list" + ] + } + + withName: 'SAMTOOLS_FAIDX' { + ext.when = { !params.fasta_fai && params.step != "annotate" } + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference/fai" }, + pattern: "*fai" + ] + } + + withName: 'TABIX_DBSNP' { + ext.when = { !params.dbsnp_tbi && params.dbsnp && (params.step == "mapping" || params.step == "markduplicates" || params.step == "prepare_recalibration") || params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('mutect2')) } + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference/dbsnp" }, + pattern: "*vcf.gz.tbi" + ] + } + + withName: 'TABIX_GERMLINE_RESOURCE' { + ext.when = { !params.germline_resource_tbi && params.germline_resource && params.tools && params.tools.split(',').contains('mutect2') } + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference/germline_resource" }, + pattern: "*vcf.gz.tbi" + ] + } + + withName: 'TABIX_KNOWN_INDELS' { + ext.when = { !params.known_indels_tbi && params.known_indels && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && params.tools.split(',').contains('haplotypecaller')) ) } + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference/known_indels" }, + pattern: "*vcf.gz.tbi" + ] + } + + withName: 'TABIX_KNOWN_SNPS' { + ext.when = { !params.known_snps_tbi && params.known_snps && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && params.tools.split(',').contains('haplotypecaller')) ) } + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference/known_snps" }, + pattern: "*vcf.gz.tbi" + ] + } + + withName: 'TABIX_PON' { + ext.when = { !params.pon_tbi && params.pon && params.tools && params.tools.split(',').contains('mutect2') } + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference/pon" }, + pattern: "*vcf.gz.tbi" + ] + } + + withName: 'UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT' { + ext.when = { params.tools && params.tools.split(',').contains('ascat')} + publishDir = [ + enabled: false + ] + } + + withName: 'UNTAR_CHR_DIR' { + ext.when = { params.tools && params.tools.split(',').contains('controlfreec')} + } +} diff --git a/conf/modules/prepare_intervals.config b/conf/modules/prepare_intervals.config new file mode 100644 index 0000000000..40b233a942 --- /dev/null +++ b/conf/modules/prepare_intervals.config @@ -0,0 +1,45 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// PREPARE INTERVALS + +process { + + withName: 'CREATE_INTERVALS_BED' { + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference/intervals" }, + pattern: "*bed" + ] + } + + withName: 'GATK4_INTERVALLISTTOBED' { + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference/intervals" }, + pattern: "*bed" + ] + } + + withName: 'TABIX_BGZIPTABIX_INTERVAL_SPLIT' { + ext.prefix = {"${meta.id}"} + publishDir = [ + enabled: params.save_reference, + mode: params.publish_dir_mode, + path: { "${params.outdir}/reference/intervals" }, + pattern: "*bed.gz" + ] + } +} diff --git a/conf/modules/prepare_recalibration.config b/conf/modules/prepare_recalibration.config new file mode 100644 index 0000000000..cb394f0a2f --- /dev/null +++ b/conf/modules/prepare_recalibration.config @@ -0,0 +1,37 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// PREPARE_RECALIBRATION + +process { + + withName: 'GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/preprocessing/" }, + pattern: "*table", + saveAs: { meta.num_intervals > 1 ? null : "recal_table/${meta.id}/${it}" } + ] + } + + withName: 'GATK4_GATHERBQSRREPORTS' { + ext.prefix = {"${meta.id}.recal"} + ext.when = { meta.num_intervals > 1 } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/preprocessing/recal_table/${meta.id}/" }, + pattern: "*table", + ] + } +} diff --git a/conf/modules/recalibrate.config b/conf/modules/recalibrate.config new file mode 100644 index 0000000000..9602e33caf --- /dev/null +++ b/conf/modules/recalibrate.config @@ -0,0 +1,61 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// RECALIBRATE + +process { + + withName: 'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" } + publishDir = [ + enabled: !params.save_output_as_bam, + mode: params.publish_dir_mode, + path: { "${params.outdir}/preprocessing/" }, + pattern: "*cram", + saveAs: { meta.num_intervals > 1 ? null : "recalibrated/${meta.id}/${it}" } + ] + } + + if ((params.step == 'mapping' || params.step == 'markduplicates'|| params.step == 'prepare_recalibration'|| params.step == 'recalibrate') && (!(params.skip_tools && params.skip_tools.split(',').contains('baserecalibrator')))) { + withName: 'NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM' { + ext.prefix = { "${meta.id}.recal" } + ext.when = { meta.num_intervals > 1 } + publishDir = [ + enabled: !params.save_output_as_bam, + mode: params.publish_dir_mode, + path: { "${params.outdir}/preprocessing/recalibrated/${meta.id}/" }, + pattern: "*cram" + ] + } + + withName: 'NFCORE_SAREK:SAREK:(BAM_APPLYBQSR|BAM_APPLYBQSR_SPARK):CRAM_MERGE_INDEX_SAMTOOLS:INDEX_CRAM' { + publishDir = [ + enabled: !params.save_output_as_bam, + mode: params.publish_dir_mode, + path: { "${params.outdir}/preprocessing/recalibrated/${meta.id}/" }, + pattern: "*{recal.cram,recal.cram.crai}" + ] + } + } + + withName: 'CRAM_TO_BAM_RECAL' { + ext.prefix = { "${meta.id}.recal" } + ext.when = { params.save_output_as_bam} + publishDir = [ + enabled: params.save_output_as_bam, + mode: params.publish_dir_mode, + path: { "${params.outdir}/preprocessing/recalibrated/${meta.id}/" }, + pattern: "*{recal.bam,recal.bam.bai}" + ] + } +} diff --git a/conf/modules/strelka.config b/conf/modules/strelka.config new file mode 100644 index 0000000000..e4fb6663db --- /dev/null +++ b/conf/modules/strelka.config @@ -0,0 +1,53 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// STRELKA + +process { + + withName: 'STRELKA_.*' { + ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.strelka" : "${meta.id}.strelka.${target_bed.simpleName}" } + ext.args = { params.wes ? "--exome" : "" } + ext.when = { params.tools && params.tools.split(',').contains('strelka') } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/" }, + pattern: "*{vcf.gz,vcf.gz.tbi}", + saveAs: { meta.num_intervals > 1 ? null : "strelka/${meta.id}/${it}" } + ] + } + + withName: 'MERGE_STRELKA.*' { + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/strelka/${meta.id}/" }, + pattern: "*{vcf.gz,vcf.gz.tbi}" + ] + } + + withName: 'MERGE_STRELKA' { + ext.prefix = {"${meta.id}.strelka.variants"} + } + + withName: 'MERGE_STRELKA_GENOME' { + ext.prefix = {"${meta.id}.strelka.genome"} + } + + // PAIR_VARIANT_CALLING + withName: 'MERGE_STRELKA_INDELS' { + ext.prefix = {"${meta.id}.strelka.somatic_indels"} + } + withName: 'MERGE_STRELKA_SNVS' { + ext.prefix = {"${meta.id}.strelka.somatic_snvs"} + } +} diff --git a/conf/modules/tiddit.config b/conf/modules/tiddit.config new file mode 100644 index 0000000000..4e8c2962ca --- /dev/null +++ b/conf/modules/tiddit.config @@ -0,0 +1,58 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// TIDDIT + +process { + + withName: 'TIDDIT_SV' { + ext.when = { params.tools && params.tools.split(',').contains('tiddit') } + ext.args = { bwa_index ? "" : "--skip_assembly" } + ext.prefix = { "${meta.id}.tiddit" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" }, + pattern: "*tab", + ] + } + + withName : 'TABIX_BGZIP_TIDDIT_SV' { + ext.prefix = { "${meta.id}.tiddit" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" }, + pattern: "*{vcf.gz,vcf.gz.tbi}" + ] + } + + // PAIR_VARIANT_CALLING + if (params.tools && params.tools.split(',').contains('tiddit')) { + withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TIDDIT:TIDDIT_NORMAL:TABIX_BGZIP_TIDDIT_SV' { + ext.prefix = {"${meta.id}.tiddit.normal"} + } + + withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TIDDIT:TIDDIT_TUMOR:TABIX_BGZIP_TIDDIT_SV' { + ext.prefix = {"${meta.id}.tiddit.tumor"} + } + + // SVDB + withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TIDDIT:SVDB_MERGE' { + ext.prefix = { "${meta.id}.tiddit" } + publishDir = [ + mode: params.publish_dir_mode, + path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" }, + pattern: "*vcf.gz" + ] + } + } +} diff --git a/conf/modules/trimming.config b/conf/modules/trimming.config new file mode 100644 index 0000000000..13aba3531d --- /dev/null +++ b/conf/modules/trimming.config @@ -0,0 +1,42 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// TRIMMING + +process { + + withName: 'FASTP' { + ext.args = [ "", + params.trim_fastq ?: "--disable_adapter_trimming", + params.clip_r1 > 0 ? "--trim_front1 ${params.clip_r1}" : "", // Remove bp from the 5' end of read 1 + params.clip_r2 > 0 ? "--trim_front2 ${params.clip_r2}" : "", // Remove bp from the 5' end of read 2 + params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed + params.three_prime_clip_r2 > 0 ? "--trim_tail2 ${params.three_prime_clip_r2}" : "", // Remove bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed + params.trim_nextseq ? "--trim_poly_g" : "", // Apply the --nextseq=X option, to trim based on quality after removing poly-G tails + params.split_fastq > 0 ? "--split_by_lines ${params.split_fastq * 4}" : "" + ].join(" ").trim() + publishDir = [ + [ + path: { "${params.outdir}/reports/fastp/${meta.sample}" }, + mode: params.publish_dir_mode, + pattern: "*.{html,json,log}" + ], + [ + enabled: params.save_trimmed || params.save_split_fastqs, + path: { "${params.outdir}/preprocessing/fastp/${meta.sample}/" }, + mode: params.publish_dir_mode, + pattern: "*.fastp.fastq.gz" + ] + ] + } +} diff --git a/conf/modules/umi.config b/conf/modules/umi.config new file mode 100644 index 0000000000..ed4f29570b --- /dev/null +++ b/conf/modules/umi.config @@ -0,0 +1,83 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Config file for defining DSL2 per module options and publishing paths +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Available keys to override module options: + ext.args = Additional arguments appended to command in module. + ext.args2 = Second set of arguments appended to command in module (multi-tool modules). + ext.args3 = Third set of arguments appended to command in module (multi-tool modules). + ext.prefix = File name prefix for output files. + ext.when = When to run the module. +---------------------------------------------------------------------------------------- +*/ + +// UMI + +process { + + withName: 'FASTQTOBAM' { + ext.prefix = {"${meta.id}"} + ext.args = { "--read-structures $params.umi_read_structure" } + publishDir = [ + //specify to avoid publishing, overwritten otherwise + enabled: false + ] + } + + withName: 'BAM2FASTQ' { + ext.args = '-T RX' + ext.when = { params.umi_read_structure } + publishDir = [ + //specify to avoid publishing, overwritten otherwise + enabled: false + ] + } + + if (params.umi_read_structure) { + withName: "NFCORE_SAREK:SAREK:FASTQ_CREATE_UMI_CONSENSUS_FGBIO:ALIGN_UMI:BWAMEM.*_MEM" { + ext.args = { "-K 100000000 -p -C -Y -R ${meta.read_group}" } + ext.args2 = '-bS' + ext.prefix = {"${meta.id}.umi_unsorted"} + publishDir = [ + //specify to avoid publishing, overwritten otherwise + enabled: false + ] + } + + withName: "NFCORE_SAREK:SAREK:FASTQ_CREATE_UMI_CONSENSUS_FGBIO:ALIGN_UMI:DRAGMAP_ALIGN" { + ext.args2 = '-bS' + ext.prefix = {"${meta.id}.umi_unsorted"} + publishDir = [ + //specify to avoid publishing, overwritten otherwise + enabled: false + ] + } + } + + withName: 'SAMBLASTER' { + ext.args = '-M --addMateTags' + ext.prefix = {"${meta.id}_unsorted_tagged"} + publishDir = [ + //specify to avoid publishing, overwritten otherwise + enabled: false + ] + } + withName: 'GROUPREADSBYUMI' { + publishDir = [ + [ path: { "${params.outdir}/reports/umi/" }, + mode: params.publish_dir_mode, + pattern: "*.{txt}" + ] + ] + } + + withName: 'CALLUMICONSENSUS' { + ext.args = '-M 1 -S Coordinate' + ext.prefix = {"${meta.id}_umi-consensus"} + publishDir = [ + path: { "${params.outdir}/preprocessing/umi/${meta.sample}" }, + mode: params.publish_dir_mode, + pattern: "*.{bam}" + ] + } +} diff --git a/conf/test.config b/conf/test/test.config similarity index 100% rename from conf/test.config rename to conf/test/test.config diff --git a/conf/test_alignment_to_fastq.config b/conf/test/test_alignment_to_fastq.config similarity index 100% rename from conf/test_alignment_to_fastq.config rename to conf/test/test_alignment_to_fastq.config diff --git a/conf/test_annotation.config b/conf/test/test_annotation.config similarity index 100% rename from conf/test_annotation.config rename to conf/test/test_annotation.config diff --git a/conf/test_full.config b/conf/test/test_full.config similarity index 100% rename from conf/test_full.config rename to conf/test/test_full.config diff --git a/conf/test_full_germline.config b/conf/test/test_full_germline.config similarity index 100% rename from conf/test_full_germline.config rename to conf/test/test_full_germline.config diff --git a/conf/test_markduplicates_bam.config b/conf/test/test_markduplicates_bam.config similarity index 100% rename from conf/test_markduplicates_bam.config rename to conf/test/test_markduplicates_bam.config diff --git a/conf/test_markduplicates_cram.config b/conf/test/test_markduplicates_cram.config similarity index 100% rename from conf/test_markduplicates_cram.config rename to conf/test/test_markduplicates_cram.config diff --git a/conf/test_no_intervals.config b/conf/test/test_no_intervals.config similarity index 100% rename from conf/test_no_intervals.config rename to conf/test/test_no_intervals.config diff --git a/conf/test_pair.config b/conf/test/test_pair.config similarity index 100% rename from conf/test_pair.config rename to conf/test/test_pair.config diff --git a/conf/test_prepare_recalibration_bam.config b/conf/test/test_prepare_recalibration_bam.config similarity index 100% rename from conf/test_prepare_recalibration_bam.config rename to conf/test/test_prepare_recalibration_bam.config diff --git a/conf/test_prepare_recalibration_cram.config b/conf/test/test_prepare_recalibration_cram.config similarity index 100% rename from conf/test_prepare_recalibration_cram.config rename to conf/test/test_prepare_recalibration_cram.config diff --git a/conf/test_recalibrate_bam.config b/conf/test/test_recalibrate_bam.config similarity index 100% rename from conf/test_recalibrate_bam.config rename to conf/test/test_recalibrate_bam.config diff --git a/conf/test_recalibrate_cram.config b/conf/test/test_recalibrate_cram.config similarity index 100% rename from conf/test_recalibrate_cram.config rename to conf/test/test_recalibrate_cram.config diff --git a/conf/test_save_bam_mapped.config b/conf/test/test_save_bam_mapped.config similarity index 100% rename from conf/test_save_bam_mapped.config rename to conf/test/test_save_bam_mapped.config diff --git a/conf/test_skip_bqsr.config b/conf/test/test_skip_bqsr.config similarity index 100% rename from conf/test_skip_bqsr.config rename to conf/test/test_skip_bqsr.config diff --git a/conf/test_skip_markduplicates.config b/conf/test/test_skip_markduplicates.config similarity index 100% rename from conf/test_skip_markduplicates.config rename to conf/test/test_skip_markduplicates.config diff --git a/conf/test_split_fastq.config b/conf/test/test_split_fastq.config similarity index 100% rename from conf/test_split_fastq.config rename to conf/test/test_split_fastq.config diff --git a/conf/test_targeted.config b/conf/test/test_targeted.config similarity index 100% rename from conf/test_targeted.config rename to conf/test/test_targeted.config diff --git a/conf/test_tools.config b/conf/test/test_tools.config similarity index 100% rename from conf/test_tools.config rename to conf/test/test_tools.config diff --git a/conf/test_tools_germline.config b/conf/test/test_tools_germline.config similarity index 100% rename from conf/test_tools_germline.config rename to conf/test/test_tools_germline.config diff --git a/conf/test_tools_somatic.config b/conf/test/test_tools_somatic.config similarity index 100% rename from conf/test_tools_somatic.config rename to conf/test/test_tools_somatic.config diff --git a/conf/test_tools_somatic_ascat.config b/conf/test/test_tools_somatic_ascat.config similarity index 100% rename from conf/test_tools_somatic_ascat.config rename to conf/test/test_tools_somatic_ascat.config diff --git a/conf/test_tools_tumoronly.config b/conf/test/test_tools_tumoronly.config similarity index 100% rename from conf/test_tools_tumoronly.config rename to conf/test/test_tools_tumoronly.config diff --git a/conf/test_trimming.config b/conf/test/test_trimming.config similarity index 100% rename from conf/test_trimming.config rename to conf/test/test_trimming.config diff --git a/conf/test_umi.config b/conf/test/test_umi.config similarity index 100% rename from conf/test_umi.config rename to conf/test/test_umi.config diff --git a/conf/test_use_gatk_spark.config b/conf/test/test_use_gatk_spark.config similarity index 100% rename from conf/test_use_gatk_spark.config rename to conf/test/test_use_gatk_spark.config diff --git a/conf/test_variantcalling_channels.config b/conf/test/test_variantcalling_channels.config similarity index 100% rename from conf/test_variantcalling_channels.config rename to conf/test/test_variantcalling_channels.config diff --git a/nextflow.config b/nextflow.config index 77f49e208a..dd886f8262 100644 --- a/nextflow.config +++ b/nextflow.config @@ -203,35 +203,35 @@ profiles { executor.name = 'local' } // Basic test profile for CI - test { includeConfig 'conf/test.config' } + test { includeConfig 'conf/test/test.config' } // Extra test profiles for full tests on AWS - test_full { includeConfig 'conf/test_full.config' } - test_full_germline { includeConfig 'conf/test_full_germline.config' } + test_full { includeConfig 'conf/test/test_full.config' } + test_full_germline { includeConfig 'conf/test/test_full_germline.config' } // Extra test profiles for more complete CI - alignment_to_fastq { includeConfig 'conf/test_alignment_to_fastq.config' } - annotation { includeConfig 'conf/test_annotation.config' } - markduplicates_bam { includeConfig 'conf/test_markduplicates_bam.config' } - markduplicates_cram { includeConfig 'conf/test_markduplicates_cram.config' } - no_intervals { includeConfig 'conf/test_no_intervals.config' } - pair { includeConfig 'conf/test_pair.config' } - prepare_recalibration_bam { includeConfig 'conf/test_prepare_recalibration_bam.config' } - prepare_recalibration_cram { includeConfig 'conf/test_prepare_recalibration_cram.config' } - recalibrate_bam { includeConfig 'conf/test_recalibrate_bam.config' } - recalibrate_cram { includeConfig 'conf/test_recalibrate_cram.config' } - save_bam_mapped { includeConfig 'conf/test_save_bam_mapped.config' } - skip_bqsr { includeConfig 'conf/test_skip_bqsr.config' } - skip_markduplicates { includeConfig 'conf/test_skip_markduplicates.config' } - split_fastq { includeConfig 'conf/test_split_fastq.config' } - targeted { includeConfig 'conf/test_targeted.config' } - tools { includeConfig 'conf/test_tools.config' } - tools_germline { includeConfig 'conf/test_tools_germline.config' } - tools_somatic { includeConfig 'conf/test_tools_somatic.config' } - tools_somatic_ascat { includeConfig 'conf/test_tools_somatic_ascat.config' } - tools_tumoronly { includeConfig 'conf/test_tools_tumoronly.config' } - trimming { includeConfig 'conf/test_trimming.config' } - umi { includeConfig 'conf/test_umi.config' } - use_gatk_spark { includeConfig 'conf/test_use_gatk_spark.config' } - variantcalling_channels { includeConfig 'conf/test_variantcalling_channels.config' } + alignment_to_fastq { includeConfig 'conf/test/test_alignment_to_fastq.config' } + annotation { includeConfig 'conf/test/test_annotation.config' } + markduplicates_bam { includeConfig 'conf/test/test_markduplicates_bam.config' } + markduplicates_cram { includeConfig 'conf/test/test_markduplicates_cram.config' } + no_intervals { includeConfig 'conf/test/test_no_intervals.config' } + pair { includeConfig 'conf/test/test_pair.config' } + prepare_recalibration_bam { includeConfig 'conf/test/test_prepare_recalibration_bam.config' } + prepare_recalibration_cram { includeConfig 'conf/test/test_prepare_recalibration_cram.config' } + recalibrate_bam { includeConfig 'conf/test/test_recalibrate_bam.config' } + recalibrate_cram { includeConfig 'conf/test/test_recalibrate_cram.config' } + save_bam_mapped { includeConfig 'conf/test/test_save_bam_mapped.config' } + skip_bqsr { includeConfig 'conf/test/test_skip_bqsr.config' } + skip_markduplicates { includeConfig 'conf/test/test_skip_markduplicates.config' } + split_fastq { includeConfig 'conf/test/test_split_fastq.config' } + targeted { includeConfig 'conf/test/test_targeted.config' } + tools { includeConfig 'conf/test/test_tools.config' } + tools_germline { includeConfig 'conf/test/test_tools_germline.config' } + tools_somatic { includeConfig 'conf/test/test_tools_somatic.config' } + tools_somatic_ascat { includeConfig 'conf/test/test_tools_somatic_ascat.config' } + tools_tumoronly { includeConfig 'conf/test/test_tools_tumoronly.config' } + trimming { includeConfig 'conf/test/test_trimming.config' } + umi { includeConfig 'conf/test/test_umi.config' } + use_gatk_spark { includeConfig 'conf/test/test_use_gatk_spark.config' } + variantcalling_channels { includeConfig 'conf/test/test_variantcalling_channels.config' } } // Load igenomes.config if required @@ -285,7 +285,39 @@ manifest { } // Load modules.config for DSL2 module specific options -includeConfig 'conf/modules.config' +includeConfig 'conf/modules/modules.config' + +// Load more modules specific config for DSL2 module specific options + +// prepare reference +includeConfig 'conf/modules/prepare_intervals.config' +includeConfig 'conf/modules/prepare_genome.config' + +// preprocessing +includeConfig 'conf/modules/alignment_to_fastq.config' +includeConfig 'conf/modules/umi.config' +includeConfig 'conf/modules/trimming.config' +includeConfig 'conf/modules/aligner.config' +includeConfig 'conf/modules/markduplicates.config' +includeConfig 'conf/modules/prepare_recalibration.config' +includeConfig 'conf/modules/recalibrate.config' + +// variant calling +includeConfig 'conf/modules/ascat.config' +includeConfig 'conf/modules/cnvkit.config' +includeConfig 'conf/modules/controlfreec.config' +includeConfig 'conf/modules/deepvariant.config' +includeConfig 'conf/modules/freebayes.config' +includeConfig 'conf/modules/haplotypecaller.config' +includeConfig 'conf/modules/manta.config' +includeConfig 'conf/modules/mpileup.config' +includeConfig 'conf/modules/msisensorpro.config' +includeConfig 'conf/modules/mutect2.config' +includeConfig 'conf/modules/strelka.config' +includeConfig 'conf/modules/tiddit.config' + +//annotate +includeConfig 'conf/modules/annotate.config' // Function to ensure that resource requirements don't go beyond // a maximum limit diff --git a/subworkflows/local/prepare_intervals/main.nf b/subworkflows/local/prepare_intervals/main.nf index 852b6ef05b..b579cab087 100644 --- a/subworkflows/local/prepare_intervals/main.nf +++ b/subworkflows/local/prepare_intervals/main.nf @@ -7,8 +7,6 @@ // A when clause condition is defined in the conf/modules.config to determine if the module should be run include { BUILD_INTERVALS } from '../../../modules/local/build_intervals/main' -include { CNVKIT_ANTITARGET } from '../../../modules/nf-core/cnvkit/antitarget/main' -include { CNVKIT_REFERENCE } from '../../../modules/nf-core/cnvkit/reference/main' include { CREATE_INTERVALS_BED } from '../../../modules/local/create_intervals_bed/main' include { GATK4_INTERVALLISTTOBED } from '../../../modules/nf-core/gatk4/intervallisttobed/main' include { TABIX_BGZIPTABIX as TABIX_BGZIPTABIX_INTERVAL_SPLIT } from '../../../modules/nf-core/tabix/bgziptabix/main' diff --git a/tests/config/pytest_tags.yml b/tests/config/pytest_tags.yml new file mode 100644 index 0000000000..465c216c48 --- /dev/null +++ b/tests/config/pytest_tags.yml @@ -0,0 +1,262 @@ +# default_extended + +default_extended: + - conf/modules/** + - modules/** + - subworkflows/** + - workflows/** + - nextflow.config + - main.nf + +# preprocessing + +## alignment_to_fastq +alignment_to_fastq: + - conf/modules/alignment_to_fastq.config + - modules/nf-core/cat/fastq/main.nf + - modules/nf-core/samtools/collatefastq/main.nf + - modules/nf-core/samtools/merge/main.nf + - modules/nf-core/samtools/view/main.nf + - subworkflows/local/bam_convert_samtools/main.nf + +## umi +umi: + - conf/modules/umi.config + - modules/nf-core/bwa/mem/main.nf + - modules/nf-core/bwamem2/mem/main.nf + - modules/nf-core/dragmap/align/main.nf + - modules/nf-core/fgbio/callmolecularconsensusreads/main.nf + - modules/nf-core/fgbio/fastqtobam/main.nf + - modules/nf-core/fgbio/groupreadsbyumi/main.nf + - modules/nf-core/samblaster/main.nf + - modules/nf-core/samtools/bam2fq/main.nf + - subworkflows/local/fastq_align_bwamem_mem2_dragmap/main.nf + - subworkflows/local/fastq_create_umi_consensus_fgbio/main.nf + +## fastp +fastp: + - conf/modules/trimming.config + - modules/nf-core/fastp/main.nf + +## aligner + +### bwamem +bwamem: + - conf/modules/aligner.config + - modules/nf-core/bwa/mem/main.nf + - subworkflows/local/fastq_align_bwamem_mem2_dragmap/main.nf + +### bwamem2 +bwamem2: + - conf/modules/aligner.config + - modules/nf-core/bwamem2/mem/main.nf + - subworkflows/local/fastq_align_bwamem_mem2_dragmap/main.nf + +### dragmap +dragmap: + - conf/modules/aligner.config + - modules/nf-core/dragmap/align/main.nf + - subworkflows/local/fastq_align_bwamem_mem2_dragmap/main.nf + +## markduplicates +markduplicates: + - conf/modules/markduplicates.config + - modules/nf-core/gatk4/markduplicates/main.nf + - modules/nf-core/mosdepth/main.nf + - modules/nf-core/samtools/convert/main.nf + - modules/nf-core/samtools/index/main.nf + - modules/nf-core/samtools/stats/main.nf + - subworkflows/local/bam_markduplicates/main.nf + - subworkflows/local/cram_qc_mosdepth_samtools/main.nf + +## prepare_recalibration +prepare_recalibration: + - conf/modules/prepare_recalibration.config + - modules/nf-core/gatk4/baserecalibrator/main.nf + - modules/nf-core/gatk4/gatherbqsrreports/main.nf + - modules/nf-core/samtools/convert/main.nf + - subworkflows/local/bam_baserecalibrator/main.nf + +## recalibrate +recalibrate: + - conf/modules/recalibrate.config + - modules/nf-core/gatk4/applybqsr/main.nf + - modules/nf-core/samtools/convert/main.nf + - modules/nf-core/samtools/index/main.nf + - modules/nf-core/samtools/merge/main.nf + - subworkflows/local/bam_applybqsr/main.nf + - subworkflows/local/cram_merge_index_samtools/main.nf + +## intervals +intervals: + - conf/modules/prepare_intervals.config + - modules/local/build_intervals/main.nf + - modules/local/create_intervals_bed/main.nf + - modules/nf-core/gatk4/intervallisttobed/main.nf + - modules/nf-core/tabix/bgziptabix/main.nf + - subworkflows/local/prepare_intervals/main.nf + +## gatk4_spark +gatk4_spark: + - conf/modules/markduplicates.config + - conf/modules/prepare_recalibration.config + - conf/modules/recalibrate.config + - modules/nf-core/gatk4/applybqsrspark/main.nf + - modules/nf-core/gatk4/baserecalibratorspark/main.nf + - modules/nf-core/gatk4/estimatelibrarycomplexity/main.nf + - modules/nf-core/gatk4/markduplicatesspark/main.nf + - subworkflows/local/bam_applybqsr_spark/main.nf + - subworkflows/local/bam_baserecalibrator_spark/main.nf + - subworkflows/local/bam_markduplicates_spark/main.nf + +# variant calling + +## cnvkit +cnvkit: + - conf/modules/cnvkit.config + - modules/nf-core/cnvkit/antitarget/main.nf + - modules/nf-core/cnvkit/batch/main.nf + - modules/nf-core/cnvkit/reference/main.nf + - subworkflows/local/bam_variant_calling_cnvkit/main.nf + - subworkflows/local/prepare_reference_cnvkit/main.nf + +## controlfreec +controlfreec: + - conf/modules/controlfreec.config + - conf/modules/mpileup.config + - modules/nf-core/cat/cat/main.nf + - modules/nf-core/controlfreec/assesssignificance/main.nf + - modules/nf-core/controlfreec/freec/main.nf + - modules/nf-core/controlfreec/freec2bed/main.nf + - modules/nf-core/controlfreec/freec2circos/main.nf + - modules/nf-core/controlfreec/makegraph/main.nf + - modules/nf-core/samtools/mpileup/main.nf + - subworkflows/local/bam_variant_calling_somatic_controlfreec/main.nf + - subworkflows/local/bam_variant_calling_tumor_only_controlfreec/main.nf + - subworkflows/local/bam_variant_calling_mpileup/main.nf + +## deepvariant +deepvariant: + - conf/modules/deepvariant.config + - modules/nf-core/deepvariant/main.nf + - modules/nf-core/gatk4/mergevcfs/main.nf + - modules/nf-core/tabix/tabix/main.nf + - subworkflows/local/bam_variant_calling_deepvariant/main.nf + +## freebayes +freebayes: + - conf/modules/freebayes.config + - modules/nf-core/bcftools/sort/main.nf + - modules/nf-core/freebayes/main.nf + - modules/nf-core/gatk4/mergevcfs/main.nf + - modules/nf-core/tabix/tabix/main.nf + - subworkflows/local/bam_variant_calling_freebayes/main.nf + +## haplotypecaller +haplotypecaller: + - conf/modules/haplotypecaller.config + - modules/nf-core/bcftools/sort/main.nf + - modules/nf-core/gatk4/applyvqsr/main.nf + - modules/nf-core/gatk4/cnnscorevariants/main.nf + - modules/nf-core/gatk4/filtervarianttranches/main.nf + - modules/nf-core/gatk4/genomicsdbimport/main.nf + - modules/nf-core/gatk4/genotypegvcfs/main.nf + - modules/nf-core/gatk4/haplotypecaller/main.nf + - modules/nf-core/gatk4/mergevcfs/main.nf + - modules/nf-core/gatk4/variantrecalibrator/main.nf + - modules/nf-core/tabix/tabix/main.nf + - subworkflows/local/bam_joint_calling_germline_gatk/main.nf + - subworkflows/local/bam_variant_calling_haplotypecaller/main.nf + - subworkflows/local/vcf_variant_filtering_gatk/main.nf + +## manta +manta: + - conf/modules/manta.config + - modules/nf-core/gatk4/mergevcfs/main.nf + - modules/nf-core/manta/germline/main.nf + - modules/nf-core/manta/somatic/main.nf + - modules/nf-core/manta/tumoronly/main.nf + - subworkflows/local/bam_variant_calling_germline_manta/main.nf + - subworkflows/local/bam_variant_calling_somatic_manta/main.nf + - subworkflows/local/bam_variant_calling_tumor_only_manta/main.nf + +## mpileup +mpileup: + - conf/modules/mpileup.config + - modules/nf-core/cat/cat/main.nf + - modules/nf-core/samtools/mpileup/main.nf + - subworkflows/local/bam_variant_calling_mpileup/main.nf + +## msisensorpro +msisensorpro: + - conf/modules/msisensorpro.config + - modules/nf-core/msisensorpro/scan/main.nf + - modules/nf-core/msisensorpro/msi_somatic/main.nf + +## mutect2 +mutect2: + - conf/modules/mutect2.config + - modules/nf-core/gatk4/calculatecontamination/main.nf + - modules/nf-core/gatk4/filtermutectcalls/main.nf + - modules/nf-core/gatk4/gatherpileupsummaries/main.nf + - modules/nf-core/gatk4/getpileupsummaries/main.nf + - modules/nf-core/gatk4/learnreadorientationmodel/main.nf + - modules/nf-core/gatk4/mergemutectstats/main.nf + - modules/nf-core/gatk4/mergevcfs/main.nf + - modules/nf-core/gatk4/mutect2/main.nf + - subworkflows/local/bam_variant_calling_somatic_mutect2/main.nf + - subworkflows/local/bam_variant_calling_tumor_only_mutect2/main.nf + +## strelka +strelka: + - conf/modules/strelka.config + - modules/nf-core/gatk4/mergevcfs/main.nf + - modules/nf-core/strelka/germline/main.nf + - modules/nf-core/strelka/somatic/main.nf + - subworkflows/local/bam_variant_calling_single_strelka/main.nf + - subworkflows/local/bam_variant_calling_somatic_strelka/main.nf + +## strelka_bp +strelka_bp: + - conf/modules/manta.config + - conf/modules/strelka.config + - modules/nf-core/gatk4/mergevcfs/main.nf + - modules/nf-core/manta/somatic/main.nf + - modules/nf-core/strelka/somatic/main.nf + - subworkflows/local/bam_variant_calling_somatic_manta/main.nf + - subworkflows/local/bam_variant_calling_somatic_strelka/main.nf + +## tiddit +tiddit: + - conf/modules/tiddit.config + - modules/nf-core/svdb/merge/main.nf.nf + - modules/nf-core/tabix/bgziptabix/main.nf + - modules/nf-core/tiddit/sv/main.nf + - subworkflows/local/bam_variant_calling_single_tiddit/main.nf + - subworkflows/local/bam_variant_calling_somatic_tiddit/main.nf + +# annotate + +## merge +merge: + - conf/modules/annotate.config + - modules/nf-core/ensemblvep/main.nf + - modules/nf-core/snpeff/main.nf + - modules/nf-core/tabix/bgziptabix/main.nf + - subworkflows/local/vcf_annotate_all/main.nf + - subworkflows/local/vcf_annotate_ensemblvep/main.nf + - subworkflows/local/vcf_annotate_snpeff/main.nf + +## snpeff +snpeff: + - conf/modules/annotate.config + - modules/nf-core/snpeff/main.nf + - modules/nf-core/tabix/bgziptabix/main.nf + - subworkflows/local/vcf_annotate_snpeff/main.nf + +## vep +vep: + - conf/modules/annotate.config + - modules/nf-core/ensemblvep/main.nf + - modules/nf-core/tabix/bgziptabix/main.nf + - subworkflows/local/vcf_annotate_ensemblvep/main.nf diff --git a/tests/test_save_mapped.yml b/tests/test_aligner_bwamem.yml similarity index 59% rename from tests/test_save_mapped.yml rename to tests/test_aligner_bwamem.yml index 81be25b685..49f6c145a9 100644 --- a/tests/test_save_mapped.yml +++ b/tests/test_aligner_bwamem.yml @@ -1,11 +1,10 @@ -- name: Run save_mapped - command: nextflow run main.nf -profile test --save_mapped +- name: Run bwamem + command: nextflow run main.nf -profile test --aligner bwa-mem --save_reference tags: + - aligner + - bwamem - preprocessing - - save_mapped files: - - path: results/csv/mapped.csv - md5sum: ae97b7394ab53a6b60921ab06c713cd9 - path: results/csv/markduplicates.csv md5sum: 0d6120bb99e92f6810343270711ca53e - path: results/csv/markduplicates_no_table.csv @@ -13,20 +12,40 @@ - path: results/csv/recalibrated.csv md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 - path: results/multiqc - - path: results/preprocessing/mapped/test/test.sorted.cram - # binary changes md5sums on reruns. - - path: results/preprocessing/mapped/test/test.sorted.cram.crai - # binary changes md5sums on reruns. - path: results/preprocessing/markduplicates/test/test.md.cram - # binary changes md5sums on reruns. + # binary changing on reruns - path: results/preprocessing/markduplicates/test/test.md.cram.crai - # binary changes md5sums on reruns. + # binary changing on reruns - path: results/preprocessing/recal_table/test/test.recal.table md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe - path: results/preprocessing/recalibrated/test/test.recal.cram - # binary changes md5sums on reruns. + # binary changing on reruns - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - # binary changes md5sums on reruns. + # binary changing on reruns + - path: results/reference/bwa/genome.amb + md5sum: 1891c1de381b3a96d4e72f590fde20c1 + - path: results/reference/bwa/genome.ann + md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969 + - path: results/reference/bwa/genome.bwt + md5sum: 815eded87e4cb6b0f1daab5c4d6e30af + - path: results/reference/bwa/genome.pac + md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070 + - path: results/reference/bwa/genome.sa + md5sum: e7cff62b919448a3a3d0fe4aaf427594 + - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi + # conda changes md5sums for test. + - path: results/reference/dict/genome.dict + md5sum: 2433fe2ba31257337bf4c4bd4cb8da15 + - path: results/reference/fai/genome.fasta.fai + md5sum: 3520cd30e1b100e55f578db9c855f685 + - path: results/reference/intervals/chr22_1-40001.bed + md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7 + - path: results/reference/intervals/chr22_1-40001.bed.gz + md5sum: d3341fa28986c40b24fcc10a079dbb80 + - path: results/reference/intervals/genome.bed + md5sum: a87dc7d20ebca626f65cc16ff6c97a3e + - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi + # conda changes md5sums for test. - path: results/reports/fastqc/test-test_L1 - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] @@ -51,6 +70,6 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: b1c2a861f64e20a94108a6de3b76c582 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 52411f93d9b5382342b40a351c2e313c + # conda changes md5sums for test. - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 811d834ff8849e69e7c5925dc2a34257 + # conda changes md5sums for test. diff --git a/tests/test_aligner_bwamem2.yml b/tests/test_aligner_bwamem2.yml new file mode 100644 index 0000000000..355d89a369 --- /dev/null +++ b/tests/test_aligner_bwamem2.yml @@ -0,0 +1,75 @@ +- name: Run bwamem2 + command: nextflow run main.nf -profile test --aligner bwa-mem2 --save_reference + tags: + - aligner + - bwamem2 + - preprocessing + files: + - path: results/csv/markduplicates.csv + md5sum: 0d6120bb99e92f6810343270711ca53e + - path: results/csv/markduplicates_no_table.csv + md5sum: 2a2d3d4842befd4def39156463859ee3 + - path: results/csv/recalibrated.csv + md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 + - path: results/multiqc + - path: results/preprocessing/markduplicates/test/test.md.cram + # binary changing on reruns + - path: results/preprocessing/markduplicates/test/test.md.cram.crai + # binary changing on reruns + - path: results/preprocessing/recal_table/test/test.recal.table + md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe + - path: results/preprocessing/recalibrated/test/test.recal.cram + # binary changing on reruns + - path: results/preprocessing/recalibrated/test/test.recal.cram.crai + # binary changing on reruns + - path: results/reference/bwamem2/genome.fasta.0123 + md5sum: d73300d44f733bcdb7c988fc3ff3e3e9 + - path: results/reference/bwamem2/genome.fasta.amb + md5sum: 1891c1de381b3a96d4e72f590fde20c1 + - path: results/reference/bwamem2/genome.fasta.ann + md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969 + - path: results/reference/bwamem2/genome.fasta.bwt.2bit.64 + md5sum: cd4bdf496eab05228a50c45ee43c1ed0 + - path: results/reference/bwamem2/genome.fasta.pac + md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070 + - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi + # conda changes md5sums for test. + - path: results/reference/dict/genome.dict + md5sum: 2433fe2ba31257337bf4c4bd4cb8da15 + - path: results/reference/fai/genome.fasta.fai + md5sum: 3520cd30e1b100e55f578db9c855f685 + - path: results/reference/intervals/chr22_1-40001.bed + md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7 + - path: results/reference/intervals/chr22_1-40001.bed.gz + md5sum: d3341fa28986c40b24fcc10a079dbb80 + - path: results/reference/intervals/genome.bed + md5sum: a87dc7d20ebca626f65cc16ff6c97a3e + - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi + # conda changes md5sums for test. + - path: results/reports/fastqc/test-test_L1 + - path: results/reports/markduplicates/test/test.md.cram.metrics + contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] + - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt + md5sum: 76fa71922a3f748e507c2364c531dfcb + - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt + md5sum: abc5df85e302b79985627888870882da + - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt + md5sum: d536456436eb275159b8c6af83213d80 + - path: results/reports/mosdepth/test/test.md.regions.bed.gz + md5sum: 38fe39894abe62e38f8ac214cba64f2b + - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi + md5sum: b1c2a861f64e20a94108a6de3b76c582 + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 76fa71922a3f748e507c2364c531dfcb + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: abc5df85e302b79985627888870882da + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: d536456436eb275159b8c6af83213d80 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: 38fe39894abe62e38f8ac214cba64f2b + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: b1c2a861f64e20a94108a6de3b76c582 + - 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. diff --git a/tests/test_aligner.yml b/tests/test_aligner_dragmap.yml similarity index 52% rename from tests/test_aligner.yml rename to tests/test_aligner_dragmap.yml index 22b2406dc8..6650f8aef1 100644 --- a/tests/test_aligner.yml +++ b/tests/test_aligner_dragmap.yml @@ -1,78 +1,3 @@ -- name: Run bwa-mem2 - command: nextflow run main.nf -profile test --aligner bwa-mem2 --save_reference - tags: - - aligner - - bwa-mem2 - - preprocessing - files: - - path: results/csv/markduplicates.csv - md5sum: 0d6120bb99e92f6810343270711ca53e - - path: results/csv/markduplicates_no_table.csv - md5sum: 2a2d3d4842befd4def39156463859ee3 - - path: results/csv/recalibrated.csv - md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 - - path: results/multiqc - - path: results/preprocessing/markduplicates/test/test.md.cram - # binary changing on reruns - - path: results/preprocessing/markduplicates/test/test.md.cram.crai - # binary changing on reruns - - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe - - path: results/preprocessing/recalibrated/test/test.recal.cram - # binary changing on reruns - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - # binary changing on reruns - - path: results/reference/bwamem2/genome.fasta.0123 - md5sum: d73300d44f733bcdb7c988fc3ff3e3e9 - - path: results/reference/bwamem2/genome.fasta.amb - md5sum: 1891c1de381b3a96d4e72f590fde20c1 - - path: results/reference/bwamem2/genome.fasta.ann - md5sum: 2df4aa2d7580639fa0fcdbcad5e2e969 - - path: results/reference/bwamem2/genome.fasta.bwt.2bit.64 - md5sum: cd4bdf496eab05228a50c45ee43c1ed0 - - path: results/reference/bwamem2/genome.fasta.pac - md5sum: 8569fbdb2c98c6fb16dfa73d8eacb070 - - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi - md5sum: 628232d0c870f2dbf73c3e81aff7b4b4 - - path: results/reference/dict/genome.dict - md5sum: 2433fe2ba31257337bf4c4bd4cb8da15 - - path: results/reference/fai/genome.fasta.fai - md5sum: 3520cd30e1b100e55f578db9c855f685 - - path: results/reference/intervals/chr22_1-40001.bed - md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7 - - path: results/reference/intervals/chr22_1-40001.bed.gz - md5sum: d3341fa28986c40b24fcc10a079dbb80 - - path: results/reference/intervals/genome.bed - md5sum: a87dc7d20ebca626f65cc16ff6c97a3e - - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi - md5sum: 1bb7ab8f22eb798efd796439d3b29b7a - - path: results/reports/fastqc/test-test_L1 - - path: results/reports/markduplicates/test/test.md.cram.metrics - contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] - - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 76fa71922a3f748e507c2364c531dfcb - - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: abc5df85e302b79985627888870882da - - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: d536456436eb275159b8c6af83213d80 - - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 38fe39894abe62e38f8ac214cba64f2b - - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: b1c2a861f64e20a94108a6de3b76c582 - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 76fa71922a3f748e507c2364c531dfcb - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: abc5df85e302b79985627888870882da - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: d536456436eb275159b8c6af83213d80 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 38fe39894abe62e38f8ac214cba64f2b - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b1c2a861f64e20a94108a6de3b76c582 - - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 52411f93d9b5382342b40a351c2e313c - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 811d834ff8849e69e7c5925dc2a34257 - name: Run dragmap command: nextflow run main.nf -profile test,docker --aligner dragmap --save_reference tags: @@ -98,7 +23,7 @@ - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changing on reruns - path: results/reference/dbsnp/dbsnp_146.hg38.vcf.gz.tbi - md5sum: 628232d0c870f2dbf73c3e81aff7b4b4 + # conda changes md5sums for test. - path: results/reference/dict/genome.dict md5sum: 2433fe2ba31257337bf4c4bd4cb8da15 - path: results/reference/dragmap/hash_table.cfg @@ -135,7 +60,7 @@ - path: results/reference/intervals/genome.bed md5sum: a87dc7d20ebca626f65cc16ff6c97a3e - path: results/reference/known_indels/mills_and_1000G.indels.vcf.gz.tbi - md5sum: 1bb7ab8f22eb798efd796439d3b29b7a + # conda changes md5sums for test. - path: results/reports/fastqc/test-test_L1 - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["LB0 13607 543 161 518779 6410 0 0 0.436262"] @@ -160,6 +85,6 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: d5f1c9389ecf52ba839e834780a94549 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 9f64e86202f2291b33c0e8c3e7981193 + # conda changes md5sums for test. - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: a63f247fb403d8679c8f96f3a128aba0 + # conda changes md5sums for test. diff --git a/tests/test_bam_remap.yml b/tests/test_alignment_to_fastq.yml similarity index 96% rename from tests/test_bam_remap.yml rename to tests/test_alignment_to_fastq.yml index b9cdf8ad8b..54d8b25b24 100644 --- a/tests/test_bam_remap.yml +++ b/tests/test_alignment_to_fastq.yml @@ -2,6 +2,7 @@ command: nextflow run main.nf -profile test,alignment_to_fastq tags: - alignment_to_fastq + - input_bam files: - path: results/csv/markduplicates.csv md5sum: 0d6120bb99e92f6810343270711ca53e @@ -44,8 +45,8 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: d0713716f63ac573f4a3385733e9a537 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: d6634d51a009e3da43b2349e424b2d9f + # conda changes md5sums for test. - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 91915547ff9e654c106a42e5edfd9405 + # conda changes md5sums for test. - path: results/preprocessing/mapped/ should_exist: false diff --git a/tests/test_annotation.yml b/tests/test_annotation_merge.yml similarity index 54% rename from tests/test_annotation.yml rename to tests/test_annotation_merge.yml index 487a2b270b..9924d41735 100644 --- a/tests/test_annotation.yml +++ b/tests/test_annotation_merge.yml @@ -1,63 +1,8 @@ -- name: Run snpEff - command: nextflow run main.nf -profile test,annotation --tools snpeff - tags: - - annotation - - snpeff - files: - - path: results/annotation/test/test_snpEff.ann.vcf.gz - md5sum: 01f24fdd76f73eefd695beea7b3d3d8e - - path: results/annotation/test/test_snpEff.ann.vcf.gz.tbi - md5sum: 51e418d9be9bb33f1d4123493b15b6c9 - - path: results/multiqc - - path: results/reports/snpeff/test/snpEff_summary.html - # snpEff_summary.html changes md5sums on reruns. - contains: [" Genome total length ", " 100,286,402 ", " MT192765.1 "] - - path: results/reports/snpeff/test/test_snpEff.csv - # test_snpEff.csv changes md5sums on reruns. - contains: - [ - "Values , 50,100", - "Count , 1,8", - "Reference , 0", - "Het , 1", - "Hom , 8", - "Missing , 0", - "MT192765.1, Position,0,1", - "MT192765.1,Count,0,0", - ] - - path: results/reports/snpeff/test/test_snpEff.genes.txt - md5sum: 130536bf0237d7f3f746d32aaa32840a -- name: Run VEP - command: nextflow run main.nf -profile test,annotation --tools vep --skip_tools multiqc - tags: - - annotation - - vep - files: - - path: results/annotation/test/test_VEP.ann.vcf.gz - # binary changes md5sums on reruns. - - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/reports/EnsemblVEP/test/test_VEP.summary.html - # test_VEP.summary.html changes md5sums on reruns. - contains: - [ - "Input filetest.vcf.gzOutput filetest_VEP.ann.vcf", - "General statistics", - "Lines of input read", - "Variants processed", - "Variants filtered out", - "Novel / existing variants", - "Overlapped genes", - "Overlapped transcripts", - "Overlapped regulatory features", - ] - name: Run snpEff followed by VEP command: nextflow run main.nf -profile test,annotation --tools merge --skip_tools multiqc tags: - annotation - merge - - snpeff - - vep files: - path: results/annotation/test/test_snpEff_VEP.ann.vcf.gz # binary changes md5sums on reruns. @@ -98,8 +43,6 @@ tags: - annotation - merge - - snpeff - - vep files: - path: results/annotation/test/test_VEP.ann.vcf.gz # binary changes md5sums on reruns. @@ -123,15 +66,3 @@ # text-based file changes md5sums on reruns. - path: results/reports/snpeff/test/test_snpEff.genes.txt md5sum: 130536bf0237d7f3f746d32aaa32840a -- name: Run VEP with fasta - command: nextflow run main.nf -profile test,annotation --tools vep --vep_include_fasta --skip_tools multiqc - tags: - - annotation - - vep - files: - - path: results/annotation/test/test_VEP.ann.vcf.gz - # binary changes md5sums on reruns. - - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/reports/EnsemblVEP/test/test_VEP.summary.html - # text-based file changes md5sums on reruns. diff --git a/tests/test_annotation_snpeff.yml b/tests/test_annotation_snpeff.yml new file mode 100644 index 0000000000..3fd4d64d69 --- /dev/null +++ b/tests/test_annotation_snpeff.yml @@ -0,0 +1,29 @@ +- name: Run snpEff + command: nextflow run main.nf -profile test,annotation --tools snpeff + tags: + - annotation + - snpeff + files: + - path: results/annotation/test/test_snpEff.ann.vcf.gz + md5sum: 01f24fdd76f73eefd695beea7b3d3d8e + - path: results/annotation/test/test_snpEff.ann.vcf.gz.tbi + md5sum: 51e418d9be9bb33f1d4123493b15b6c9 + - path: results/multiqc + - path: results/reports/snpeff/test/snpEff_summary.html + # snpEff_summary.html changes md5sums on reruns. + contains: [" Genome total length ", " 100,286,402 ", " MT192765.1 "] + - path: results/reports/snpeff/test/test_snpEff.csv + # test_snpEff.csv changes md5sums on reruns. + contains: + [ + "Values , 50,100", + "Count , 1,8", + "Reference , 0", + "Het , 1", + "Hom , 8", + "Missing , 0", + "MT192765.1, Position,0,1", + "MT192765.1,Count,0,0", + ] + - path: results/reports/snpeff/test/test_snpEff.genes.txt + md5sum: 130536bf0237d7f3f746d32aaa32840a diff --git a/tests/test_annotation_vep.yml b/tests/test_annotation_vep.yml new file mode 100644 index 0000000000..6c55f8c3d1 --- /dev/null +++ b/tests/test_annotation_vep.yml @@ -0,0 +1,28 @@ +- name: Run VEP + command: nextflow run main.nf -profile test,annotation --tools vep --skip_tools multiqc + tags: + - annotation + - vep + files: + - path: results/annotation/test/test_VEP.ann.vcf.gz + # binary changes md5sums on reruns. + - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi + md5sum: 4cb176febbc8c26d717a6c6e67b9c905 + - path: results/reports/EnsemblVEP/test/test_VEP.summary.html + # test_VEP.summary.html changes md5sums on reruns. + contains: + ["Input filetest.vcf.gzOutput filetest_VEP.ann.vcf"] +- name: Run VEP with fasta + command: nextflow run main.nf -profile test,annotation --tools vep --vep_include_fasta --skip_tools multiqc + tags: + - annotation + - vep + files: + - path: results/annotation/test/test_VEP.ann.vcf.gz + # binary changes md5sums on reruns. + - path: results/annotation/test/test_VEP.ann.vcf.gz.tbi + md5sum: 4cb176febbc8c26d717a6c6e67b9c905 + - path: results/reports/EnsemblVEP/test/test_VEP.summary.html + # text-based file changes md5sums on reruns. + contains: + ["Input filetest.vcf.gzOutput filetest_VEP.ann.vcf"] diff --git a/tests/test_cnvkit.yml b/tests/test_cnvkit.yml new file mode 100644 index 0000000000..930d2cae94 --- /dev/null +++ b/tests/test_cnvkit.yml @@ -0,0 +1,158 @@ +- name: Run variant calling on somatic samples with cnvkit + command: nextflow run main.nf -profile test,tools_somatic --tools cnvkit + tags: + - cnvkit + - copy_number_calling + - somatic + - variant_calling + files: + - path: results/multiqc + - path: results/variant_calling/cnvkit/sample3/multi_intervals.antitarget.bed + md5sum: 3d4d20f9f23b39970865d29ef239d20b + - path: results/variant_calling/cnvkit/sample3/multi_intervals.target.bed + md5sum: 86d30493bb2e619a93f4ebc2923d29f3 + - path: results/variant_calling/cnvkit/sample3/reference.cnn + md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec + - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted-diagram.pdf + # binary changes md5sums on reruns. + - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted-scatter.png + # conda changes md5sums for test. + - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn + md5sum: fe1248aa91fad7769303bb4c031d55ca + - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.bintest.cns + md5sum: e55667a75d7d8eaec2efd3b611f15379 + - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.call.cns + md5sum: 9968e02ef2f11ed22e2789c053f7159c + - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.cnr + md5sum: 3f0fe46574d0f7137f779e7ac1c2362d + - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.cns + md5sum: 0b2b81d391965488b8634a2b802b69cd + - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.targetcoverage.cnn + md5sum: 79aae7e9c135fb8c65f8fbda12610faf + - path: results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.antitarget.bed + md5sum: 3d4d20f9f23b39970865d29ef239d20b + - path: results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.target.bed + md5sum: 86d30493bb2e619a93f4ebc2923d29f3 + - path: results/variant_calling/cnvkit/sample4_vs_sample3/reference.cnn + md5sum: 59ec306bb820684b1f6f277d67cb2d92 + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn + md5sum: fe1248aa91fad7769303bb4c031d55ca + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test.paired_end.recalibrated.sorted.targetcoverage.cnn + md5sum: 79aae7e9c135fb8c65f8fbda12610faf + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted-diagram.pdf + # binary changes md5sums on reruns. + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted-scatter.png + # conda changes md5sums for test. + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn + md5sum: 067115082c4af4b64d58c0dc3a3642e4 + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.bintest.cns + md5sum: e9a260b81a34d8bc75330435d2a5e8da + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.call.cns + md5sum: c7d7fd87b27e103f73988ae307450e82 + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cnr + md5sum: 26c506866198d46610c71fa6c0f9e381 + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cns + md5sum: 83510b274c24a2671a962477a1ceb436 + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn + md5sum: b4a49faf170e436ec32dcc21ccc3ce8f + - path: results/cnvkit + should_exist: false +- name: Run variant calling on tumor_only sample with cnvkit + command: nextflow run main.nf -profile test,tools_tumoronly --tools cnvkit + tags: + - cnvkit + - copy_number_calling + - tumor_only + - variant_calling + files: + - path: results/multiqc + - path: results/variant_calling/cnvkit/sample2/cnvkit.reference.antitarget-tmp.bed + md5sum: 3d4d20f9f23b39970865d29ef239d20b + - path: results/variant_calling/cnvkit/sample2/cnvkit.reference.target-tmp.bed + md5sum: 657b25dbda8516624efa8cb2cf3716ca + - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted-diagram.pdf + # binary changes md5sums on reruns. + - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted-scatter.png + # conda changes md5sums for test. + - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn + md5sum: 067115082c4af4b64d58c0dc3a3642e4 + - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.bintest.cns + md5sum: f6adc75a0a86b7a921eca1b79a394cb0 + - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.call.cns + md5sum: f7caeca04aba28b125ce26b511f42afb + - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.cnr + md5sum: d9bdb71ce807051369577ee7f807a40c + - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.cns + md5sum: 2b56aac606ba6183d018b30ca58afcec + - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.targetcoverage.cnn + md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3 + - path: results/cnvkit + should_exist: false +- name: Run variant calling on germline sample with cnvkit + command: nextflow run main.nf -profile test,tools_germline --tools cnvkit + tags: + - cnvkit + - copy_number_calling + - germline + - variant_calling + files: + - path: results/multiqc + - path: results/variant_calling/cnvkit/sample1/multi_intervals.antitarget.bed + md5sum: 3d4d20f9f23b39970865d29ef239d20b + - path: results/variant_calling/cnvkit/sample1/multi_intervals.target.bed + md5sum: 86d30493bb2e619a93f4ebc2923d29f3 + - path: results/variant_calling/cnvkit/sample1/reference.cnn + md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec + - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted-diagram.pdf + # binary changes md5sums on reruns. + - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted-scatter.png + # conda changes md5sums for test. + - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn + md5sum: fe1248aa91fad7769303bb4c031d55ca + - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.bintest.cns + md5sum: e55667a75d7d8eaec2efd3b611f15379 + - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.call.cns + md5sum: 9968e02ef2f11ed22e2789c053f7159c + - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.cnr + md5sum: 3f0fe46574d0f7137f779e7ac1c2362d + - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.cns + md5sum: 0b2b81d391965488b8634a2b802b69cd + - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.targetcoverage.cnn + md5sum: 79aae7e9c135fb8c65f8fbda12610faf + - path: results/cnvkit + should_exist: false +- name: Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal + command: nextflow run main.nf -profile test,tools_somatic --tools cnvkit --only_paired_variant_calling + tags: + - cnvkit + - somatic + - only_paired_variant_calling + - copy_number_calling + files: + - path: results/multiqc + - path: results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.antitarget.bed + md5sum: 3d4d20f9f23b39970865d29ef239d20b + - path: results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.target.bed + md5sum: 86d30493bb2e619a93f4ebc2923d29f3 + - path: results/variant_calling/cnvkit/sample4_vs_sample3/reference.cnn + md5sum: 59ec306bb820684b1f6f277d67cb2d92 + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn + md5sum: fe1248aa91fad7769303bb4c031d55ca + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test.paired_end.recalibrated.sorted.targetcoverage.cnn + md5sum: 79aae7e9c135fb8c65f8fbda12610faf + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted-diagram.pdf + # binary changes md5sums on reruns. + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted-scatter.png + # conda changes md5sums for test. + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn + md5sum: 067115082c4af4b64d58c0dc3a3642e4 + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.bintest.cns + md5sum: e9a260b81a34d8bc75330435d2a5e8da + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.call.cns + md5sum: c7d7fd87b27e103f73988ae307450e82 + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cnr + md5sum: 26c506866198d46610c71fa6c0f9e381 + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cns + md5sum: 83510b274c24a2671a962477a1ceb436 + - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn + md5sum: b4a49faf170e436ec32dcc21ccc3ce8f diff --git a/tests/test_controlfreec.yml b/tests/test_controlfreec.yml new file mode 100644 index 0000000000..5f3ea7f452 --- /dev/null +++ b/tests/test_controlfreec.yml @@ -0,0 +1,150 @@ +- name: Run variant calling on somatic samples with controlfreec + command: nextflow run main.nf -profile test,tools_somatic --tools controlfreec + tags: + - controlfreec + - somatic + - variant_calling + - copy_number_calling + files: + - path: results/multiqc + - path: results/untar/chromosomes/chr21.fasta + md5sum: 69bd44ef67566a76d6cbb8aa4a25ae35 + - path: results/variant_calling/controlfreec/sample4_vs_sample3/config.txt + contains: + [ + "BedGraphOutput = TRUE", + "minExpectedGC = 0", + "maxThreads = 2", + "noisyData = TRUE", + "readCountThreshold = 1", + "sex = XX", + "window = 10", + ] + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.bed + md5sum: 833920178e4f40a296d8eab029caf086 + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.circos.txt + md5sum: 92ce5ce97b27a7214dfa9c2cb20cf854 + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz_control.cpn + md5sum: 508a003da85b186d9a60d867ef7cdf15 + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.p.value.txt + # binary changes md5sums on reruns. + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_BAF.txt + # binary changes md5sums on reruns. + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_CNVs + # binary changes md5sums on reruns. + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_info.txt + md5sum: 271271719c576d9218bdc859850e54ee + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_ratio.BedGraph + md5sum: 5d3321af93678f16878d59e01d3a87d3 + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_ratio.txt + # binary changes md5sums on reruns. + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_sample.cpn + md5sum: befe1706c61464635a76c7323a6bd2a2 + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.png + # binary changes md5sums on reruns. + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.log2.png + # binary changes md5sums on reruns. + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.png + # binary changes md5sums on reruns. + - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz + # binary changes md5sums on reruns. + - path: results/cnvkit + should_exist: false +- name: Run variant calling on somatic samples with controlfreec without intervals + command: nextflow run main.nf -profile test,tools_somatic --tools controlfreec --no_intervals -stub-run + tags: + - controlfreec + - no_intervals + - somatic + - variant_calling + - copy_number_calling + files: + - 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/untar/chromosomes + - path: results/variant_calling/controlfreec/sample4_vs_sample3/GC_profile.sample4_vs_sample3.cpn + md5sum: d41d8cd98f00b204e9800998ecf8427e # This is the md5sum of an empty file. Are all these files suppose to be empty? + - path: results/variant_calling/controlfreec/sample4_vs_sample3/config.txt + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.bed + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.circos.txt + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.p.value.txt + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.png + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.txt + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_CNVs + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_info.txt + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.BedGraph + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.log2.png + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.png + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.txt + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_sample.cpn + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz + # binary changes md5sums on reruns. + - path: results/controlfreec + should_exist: false + - path: results/mpileup + should_exist: false +- name: Run variant calling on tumor_only sample with controlfreec + command: nextflow run main.nf -profile test,tools_tumoronly --tools controlfreec -stub-run + tags: + - controlfreec + - tumor_only + - variant_calling + - copy_number_calling + files: + - path: results/multiqc + - path: results/variant_calling/controlfreec/sample2/GC_profile.sample2.cpn + md5sum: d41d8cd98f00b204e9800998ecf8427e # This is the md5sum of an empty file. Are all these files suppose to be empty? + - path: results/variant_calling/controlfreec/sample2/config.txt + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample2/sample2.bed + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample2/sample2.circos.txt + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample2/sample2.p.value.txt + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample2/sample2_BAF.png + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample2/sample2_BAF.txt + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample2/sample2_CNVs + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample2/sample2_info.txt + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample2/sample2_ratio.BedGraph + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample2/sample2_ratio.log2.png + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample2/sample2_ratio.png + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample2/sample2_ratio.txt + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/controlfreec/sample2/sample2_sample.cpn + md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: results/variant_calling/mpileup/sample2/sample2.tumor.mpileup.gz + # binary changes md5sums on reruns. + - path: results/controlfreec + should_exist: false + - path: results/mpileup + should_exist: false diff --git a/tests/test_deepvariant.yml b/tests/test_deepvariant.yml new file mode 100644 index 0000000000..5cc462a74a --- /dev/null +++ b/tests/test_deepvariant.yml @@ -0,0 +1,59 @@ +- name: Run variant calling on germline sample with deepvariant + command: nextflow run main.nf -profile test,tools_germline --tools deepvariant + tags: + - deepvariant + - germline + - variant_calling + files: + - path: results/multiqc + - path: results/reports/bcftools/deepvariant/sample1/sample1.deepvariant.bcftools_stats.txt + md5sum: 433aa535e9ce72acddca7be36b12238b + - path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.FILTER.summary + md5sum: f97d30123c7e20c704e9a8a73170661e + - path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.TsTv.count + md5sum: 1f546d259ddc493736507b35ee520dc4 + - path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.TsTv.qual + md5sum: 437d6a802b10f05fa1601166eb6b7d48 + - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/deepvariant + should_exist: false +- name: Run variant calling on germline sample with deepvariant without intervals + command: nextflow run main.nf -profile test,tools_germline --tools deepvariant --no_intervals + tags: + - deepvariant + - germline + - no_intervals + - variant_calling + files: + - 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/deepvariant/sample1/sample1.deepvariant.bcftools_stats.txt + md5sum: 0d8602284347cb5acf1c264a301f5093 + - path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.FILTER.summary + md5sum: cffb486232d067db80616c3129bf1322 + - path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.TsTv.count + md5sum: bbd541f33c490df06fee5feb2f6e2c7f + - path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.TsTv.qual + md5sum: 037063e030edec5fb4e784b1f6c8954f + - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/deepvariant + should_exist: false diff --git a/tests/test_default.yml b/tests/test_default.yml index a106028b87..5d808516ee 100644 --- a/tests/test_default.yml +++ b/tests/test_default.yml @@ -3,6 +3,7 @@ tags: - default - preprocessing + - variant_calling files: - path: results/csv/markduplicates.csv md5sum: 0d6120bb99e92f6810343270711ca53e diff --git a/tests/test_default_extended.yml b/tests/test_default_extended.yml new file mode 100644 index 0000000000..86386bfb12 --- /dev/null +++ b/tests/test_default_extended.yml @@ -0,0 +1,446 @@ +- name: Run save_mapped + command: nextflow run main.nf -profile test --save_mapped + tags: + - default_extended + - preprocessing + - save_mapped + - variant_calling + files: + - path: results/csv/mapped.csv + md5sum: ae97b7394ab53a6b60921ab06c713cd9 + - path: results/csv/markduplicates.csv + md5sum: 0d6120bb99e92f6810343270711ca53e + - path: results/csv/markduplicates_no_table.csv + md5sum: 2a2d3d4842befd4def39156463859ee3 + - path: results/csv/recalibrated.csv + md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 + - path: results/multiqc + - path: results/preprocessing/mapped/test/test.sorted.cram + # binary changes md5sums on reruns. + - path: results/preprocessing/mapped/test/test.sorted.cram.crai + # binary changes md5sums on reruns. + - 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: 4ac774bf5f1157e77426fd82f5ac0fbe + - 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/fastqc/test-test_L1 + - path: results/reports/markduplicates/test/test.md.cram.metrics + contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] + - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt + md5sum: 76fa71922a3f748e507c2364c531dfcb + - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt + md5sum: abc5df85e302b79985627888870882da + - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt + md5sum: d536456436eb275159b8c6af83213d80 + - path: results/reports/mosdepth/test/test.md.regions.bed.gz + md5sum: 38fe39894abe62e38f8ac214cba64f2b + - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi + md5sum: b1c2a861f64e20a94108a6de3b76c582 + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 76fa71922a3f748e507c2364c531dfcb + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: abc5df85e302b79985627888870882da + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: d536456436eb275159b8c6af83213d80 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: 38fe39894abe62e38f8ac214cba64f2b + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: b1c2a861f64e20a94108a6de3b76c582 + - 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/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: dd87f507da7de20d5318841af312493b + - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count + md5sum: fa27f678965b7cba6a92efcd039f802a + - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual + md5sum: bc68ae4e688e9fb772b457069e604883 + - 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 + - path: results/strelka + should_exist: false +- name: Run save_output_as_bam + command: nextflow run main.nf -profile test --save_output_as_bam + tags: + - default_extended + - preprocessing + - save_output_as_bam + - variant_calling + files: + - path: results/csv/markduplicates.csv + md5sum: 8679570b8db1937ee574fec36b25d7bc + - path: results/csv/markduplicates_no_table.csv + md5sum: 145154b6037e90448273fbe8e8dec5d3 + - path: results/csv/recalibrated.csv + md5sum: 3ddc20eb105fdcc483945afd7d7d238c + - path: results/multiqc + - path: results/preprocessing/markduplicates/test/test.md.bam.bai + # conda changes md5sums for test. + - path: results/preprocessing/markduplicates/test/test.md.bam + # conda changes md5sums for test. + - path: results/preprocessing/recal_table/test/test.recal.table + md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe + - path: results/preprocessing/recalibrated/test/test.recal.bam + # binary changes md5sums on reruns. + - path: results/preprocessing/recalibrated/test/test.recal.bam.bai + # binary changes md5sums on reruns. + - path: results/reports/fastqc/test-test_L1 + - path: results/reports/markduplicates/test/test.md.cram.metrics + contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] + - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt + md5sum: 76fa71922a3f748e507c2364c531dfcb + - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt + md5sum: abc5df85e302b79985627888870882da + - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt + md5sum: d536456436eb275159b8c6af83213d80 + - path: results/reports/mosdepth/test/test.md.regions.bed.gz + md5sum: 38fe39894abe62e38f8ac214cba64f2b + - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi + md5sum: b1c2a861f64e20a94108a6de3b76c582 + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 76fa71922a3f748e507c2364c531dfcb + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: abc5df85e302b79985627888870882da + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: d536456436eb275159b8c6af83213d80 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: 38fe39894abe62e38f8ac214cba64f2b + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: b1c2a861f64e20a94108a6de3b76c582 + - 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/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: dd87f507da7de20d5318841af312493b + - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count + md5sum: fa27f678965b7cba6a92efcd039f802a + - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual + md5sum: bc68ae4e688e9fb772b457069e604883 + - 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 + - path: results/strelka + should_exist: false +- name: Run default pipeline with skipping Markduplicates + command: nextflow run main.nf -profile test,skip_markduplicates + tags: + - default_extended + - preprocessing + - skip_markduplicates + files: + - path: results/csv/mapped.csv + md5sum: ae97b7394ab53a6b60921ab06c713cd9 + - path: results/csv/recalibrated.csv + md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 + - path: results/multiqc + - path: results/preprocessing/mapped/test/test.sorted.cram + # binary changes md5sums on reruns. + - path: results/preprocessing/mapped/test/test.sorted.cram.crai + # binary changes md5sums on reruns. + - path: results/preprocessing/recal_table/test/test.recal.table + md5sum: 8de213f4c00fac61a1102633760493df + - 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/fastqc/test-test_L1 + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 48aa760b024d7c0ddd5a66f89a1cb544 + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: 71e938314bba70f978271b2b56cb7ad3 + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: 0786d56af0672eaef44b29f4ed5c12cb + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: b8719430e56a58f734884bb422a7b8fa + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: e3235323f455414ee3acc7144e659caf + - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt + md5sum: 48aa760b024d7c0ddd5a66f89a1cb544 + - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt + md5sum: 71e938314bba70f978271b2b56cb7ad3 + - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt + md5sum: 0786d56af0672eaef44b29f4ed5c12cb + - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz + md5sum: b8719430e56a58f734884bb422a7b8fa + - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi + md5sum: e3235323f455414ee3acc7144e659caf + - 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 +- name: Run default pipeline with skipping Markduplicates with save_mapped + command: nextflow run main.nf -profile test,skip_markduplicates --save_mapped + tags: + - default_extended + - preprocessing + - save_mapped + files: + - path: results/csv/mapped.csv + md5sum: ae97b7394ab53a6b60921ab06c713cd9 + - path: results/csv/recalibrated.csv + md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 + - path: results/multiqc + - path: results/preprocessing/mapped/test/test.sorted.cram + # binary changes md5sums on reruns. + - path: results/preprocessing/mapped/test/test.sorted.cram.crai + # binary changes md5sums on reruns. + - path: results/preprocessing/recal_table/test/test.recal.table + md5sum: 8de213f4c00fac61a1102633760493df + - 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/fastqc/test-test_L1 + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 48aa760b024d7c0ddd5a66f89a1cb544 + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: 71e938314bba70f978271b2b56cb7ad3 + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: 0786d56af0672eaef44b29f4ed5c12cb + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: b8719430e56a58f734884bb422a7b8fa + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: e3235323f455414ee3acc7144e659caf + - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt + md5sum: 48aa760b024d7c0ddd5a66f89a1cb544 + - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt + md5sum: 71e938314bba70f978271b2b56cb7ad3 + - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt + md5sum: 0786d56af0672eaef44b29f4ed5c12cb + - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz + md5sum: b8719430e56a58f734884bb422a7b8fa + - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi + md5sum: e3235323f455414ee3acc7144e659caf + - 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 +- name: Run default pipeline with skipping Markduplicates with save_mapped & save_output_as_bam + command: nextflow run main.nf -profile test,skip_markduplicates --save_mapped --save_output_as_bam + tags: + - default_extended + - preprocessing + - save_output_as_bam + files: + - path: results/csv/mapped.csv + md5sum: 7f21bf40d3fbc248ee2ea3fdf0f7cdb2 + - path: results/csv/recalibrated.csv + md5sum: 3ddc20eb105fdcc483945afd7d7d238c + - path: results/multiqc + - path: results/preprocessing/mapped/test/test.sorted.bam + # binary changes md5sums on reruns. + - path: results/preprocessing/mapped/test/test.sorted.bam.bai + # binary changes md5sums on reruns. + - path: results/preprocessing/recal_table/test/test.recal.table + md5sum: 8de213f4c00fac61a1102633760493df + - path: results/preprocessing/recalibrated/test/test.recal.bam + # binary changes md5sums on reruns. + - path: results/preprocessing/recalibrated/test/test.recal.bam.bai + # binary changes md5sums on reruns. + - path: results/reports/fastqc/test-test_L1 + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 48aa760b024d7c0ddd5a66f89a1cb544 + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: 71e938314bba70f978271b2b56cb7ad3 + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: 0786d56af0672eaef44b29f4ed5c12cb + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: b8719430e56a58f734884bb422a7b8fa + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: e3235323f455414ee3acc7144e659caf + - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt + md5sum: 48aa760b024d7c0ddd5a66f89a1cb544 + - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt + md5sum: 71e938314bba70f978271b2b56cb7ad3 + - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt + md5sum: 0786d56af0672eaef44b29f4ed5c12cb + - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz + md5sum: b8719430e56a58f734884bb422a7b8fa + - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi + md5sum: e3235323f455414ee3acc7144e659caf + - 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 +- name: Run default pipeline with skipping all QC steps + command: nextflow run main.nf -profile test --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools + tags: + - default_extended + - preprocessing + - skip_qc + - variant_calling + files: + - path: results/csv/markduplicates.csv + md5sum: 0d6120bb99e92f6810343270711ca53e + - path: results/csv/markduplicates_no_table.csv + md5sum: 2a2d3d4842befd4def39156463859ee3 + - path: results/csv/recalibrated.csv + md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 + - 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: 4ac774bf5f1157e77426fd82f5ac0fbe + - 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/multiqc + should_exist: false + - path: results/reports/fastqc + should_exist: false + - path: results/reports/markduplicates + should_exist: false + - path: results/reports/mosdepth + should_exist: false + - path: results/reports/samtools + should_exist: false + - 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: dd87f507da7de20d5318841af312493b + - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.count + md5sum: fa27f678965b7cba6a92efcd039f802a + - path: results/reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual + md5sum: bc68ae4e688e9fb772b457069e604883 + - 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 + - path: results/strelka + should_exist: false +- name: Run default pipeline for tumor normal pair + command: nextflow run main.nf -profile test,pair + tags: + - default_extended + - preprocessing + - tumor_normal_pair + files: + - path: results/csv/markduplicates.csv + md5sum: e8e587ac25253ff7ab8f1cc66d410c98 + - path: results/csv/markduplicates_no_table.csv + md5sum: 617574c9b607e5daaf4ad56d48982247 + - path: results/csv/recalibrated.csv + md5sum: 008dff17e2a0d96ef9c1cae12fcab6ab + - 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: 4ac774bf5f1157e77426fd82f5ac0fbe + - 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/preprocessing/markduplicates/test2/test2.md.cram + # binary changes md5sums on reruns. + - path: results/preprocessing/markduplicates/test2/test2.md.cram.crai + # binary changes md5sums on reruns. + - path: results/preprocessing/recal_table/test2/test2.recal.table + md5sum: 0626cd4337eab79b38b5bc5c95e0c003 + - path: results/preprocessing/recalibrated/test2/test2.recal.cram + # binary changes md5sums on reruns. + - path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai + # binary changes md5sums on reruns. + - path: results/reports/fastqc/test-test_L1 + - path: results/reports/fastqc/test2-test_L1 + - path: results/reports/markduplicates/test/test.md.cram.metrics + contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] + - path: results/reports/markduplicates/test2/test2.md.cram.metrics + contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"] + - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt + md5sum: 76fa71922a3f748e507c2364c531dfcb + - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt + md5sum: abc5df85e302b79985627888870882da + - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt + md5sum: d536456436eb275159b8c6af83213d80 + - path: results/reports/mosdepth/test/test.md.regions.bed.gz + md5sum: 38fe39894abe62e38f8ac214cba64f2b + - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi + md5sum: b1c2a861f64e20a94108a6de3b76c582 + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 76fa71922a3f748e507c2364c531dfcb + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: abc5df85e302b79985627888870882da + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: d536456436eb275159b8c6af83213d80 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: 38fe39894abe62e38f8ac214cba64f2b + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: b1c2a861f64e20a94108a6de3b76c582 + - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt + md5sum: 2020cf6dfc7ddca020c921dd9f0549b7 + - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt + md5sum: 38ff8b38c33b9231f047fea8ea830aae + - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt + md5sum: 8b991358768cade225470a07cd34f573 + - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz + md5sum: 5d67bc6ea9f077abb4fdac3b087c6387 + - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi + md5sum: d5f1c9389ecf52ba839e834780a94549 + - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt + md5sum: 2020cf6dfc7ddca020c921dd9f0549b7 + - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt + md5sum: 38ff8b38c33b9231f047fea8ea830aae + - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt + md5sum: 8b991358768cade225470a07cd34f573 + - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz + md5sum: 5d67bc6ea9f077abb4fdac3b087c6387 + - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi + md5sum: d5f1c9389ecf52ba839e834780a94549 + - path: results/reports/samtools/test/test.md.cram.stats + # conda changes md5sums for test. + - path: results/reports/samtools/test/test.recal.cram.stats + # conda changes md5sums for test. + - path: results/reports/samtools/test2/test2.md.cram.stats + # conda changes md5sums for test. + - path: results/reports/samtools/test2/test2.recal.cram.stats + # conda changes md5sums for test. + - path: results/preprocessing/mapped/ + should_exist: false diff --git a/tests/test_fastp.yml b/tests/test_fastp.yml new file mode 100644 index 0000000000..985ef5cc7d --- /dev/null +++ b/tests/test_fastp.yml @@ -0,0 +1,115 @@ +- name: Run trimming pipeline + command: nextflow run main.nf -profile test,trimming --save_trimmed + tags: + - fastp + - preprocessing + - trimming + files: + - path: results/csv/markduplicates.csv + md5sum: 0d6120bb99e92f6810343270711ca53e + - path: results/csv/markduplicates_no_table.csv + md5sum: 2a2d3d4842befd4def39156463859ee3 + - path: results/csv/recalibrated.csv + md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 + - path: results/multiqc + - path: results/preprocessing/fastp/test/test-test_L1_1.fastp.fastq.gz + # conda changes md5sums for test. + - path: results/preprocessing/fastp/test/test-test_L1_2.fastp.fastq.gz + # conda changes md5sums for test. + - 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: 766a4cd88d3d085c19d8e31540040ecd + - 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/fastp/test + - path: results/reports/fastqc/test-test_L1 + - path: results/reports/markduplicates/test/test.md.cram.metrics + contains: ["test 8304 930 80 523308 3813 0 0 0.375148", "1.0 930 930"] + - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt + md5sum: 626d5c03a6192283a302bde72415c693 + - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt + md5sum: 4a82e0e19a549edae27fc0cc71f6546f + - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt + md5sum: 51e054d8b3b4ef745c94fbda7a2ef2f3 + - path: results/reports/mosdepth/test/test.md.regions.bed.gz + md5sum: 80738b824b3a7d00bdad2d8e26ac3ccc + - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi + md5sum: a5ad8f917979f62eacfff1461529dbaa + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 626d5c03a6192283a302bde72415c693 + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: 4a82e0e19a549edae27fc0cc71f6546f + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: 51e054d8b3b4ef745c94fbda7a2ef2f3 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: 80738b824b3a7d00bdad2d8e26ac3ccc + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: a5ad8f917979f62eacfff1461529dbaa + - path: results/reports/samtools/test/test.md.cram.stats + # conda changes md5sums for test. + - path: results/reports/samtools/test/test.recal.cram.stats + # conda changes md5sums for test. +- name: Run split fastq module + command: nextflow run main.nf -profile test,split_fastq + tags: + - fastp + - preprocessing + - split_fastq + files: + - path: results/csv/markduplicates.csv + md5sum: 0d6120bb99e92f6810343270711ca53e + - path: results/csv/markduplicates_no_table.csv + md5sum: 2a2d3d4842befd4def39156463859ee3 + - path: results/csv/recalibrated.csv + md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 + - path: results/preprocessing/fastp/test/0001.test-test_L1_1.fastp.fastq.gz + # conda changes md5sums for test. + - path: results/preprocessing/fastp/test/0001.test-test_L1_2.fastp.fastq.gz + # conda changes md5sums for test. + - path: results/preprocessing/fastp/test/0002.test-test_L1_1.fastp.fastq.gz + # conda changes md5sums for test. + - path: results/preprocessing/fastp/test/0002.test-test_L1_2.fastp.fastq.gz + # conda changes md5sums for test. + - 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: 36b9cec9f69726d3acb0b42685100eb2 + - 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/fastp/test + - path: results/reports/fastqc/test-test_L1 + - path: results/reports/markduplicates/test/test.md.cram.metrics + contains: ["test 8741 445 85 523841 3811 0 0 0.395701", "1.0 445 445"] + - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt + md5sum: 3fae37c0bcc0742b89a5b5d01978f593 + - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt + md5sum: 2d5a9d4f8a19ec0aa962ee5912a506c2 + - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt + md5sum: 970e3faef6be251e32b3af06ed7f5cfc + - path: results/reports/mosdepth/test/test.md.regions.bed.gz + md5sum: 1903e2eedef8d11176fb30d0bb934b13 + - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi + md5sum: 1b65ac38cd96783394e0cf9b7bdd5bc2 + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 3fae37c0bcc0742b89a5b5d01978f593 + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: 2d5a9d4f8a19ec0aa962ee5912a506c2 + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: 970e3faef6be251e32b3af06ed7f5cfc + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: 1903e2eedef8d11176fb30d0bb934b13 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: 1b65ac38cd96783394e0cf9b7bdd5bc2 + - 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. diff --git a/tests/test_freebayes.yml b/tests/test_freebayes.yml new file mode 100644 index 0000000000..245f81250f --- /dev/null +++ b/tests/test_freebayes.yml @@ -0,0 +1,413 @@ +- name: Run variant calling on germline sample with freebayes + command: nextflow run main.nf -profile test,targeted --tools freebayes + tags: + - freebayes + - germline + - variant_calling + files: + - path: results/csv/markduplicates.csv + md5sum: 0d6120bb99e92f6810343270711ca53e + - path: results/csv/markduplicates_no_table.csv + md5sum: 2a2d3d4842befd4def39156463859ee3 + - path: results/csv/recalibrated.csv + md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 + - path: results/csv/variantcalled.csv + md5sum: 0cc6a67fedb2ef9ce97e463d310f9f30 + - 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: c990e4f1b7dbd5a3a623882a54ae2bf2 + - 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/bcftools/freebayes/test/test.freebayes.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/fastqc/test-test_L1 + - path: results/reports/markduplicates/test/test.md.cram.metrics + contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] + - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt + md5sum: 5a0679057c530e5945c9c5a3a17312dc + - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt + md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 + - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt + md5sum: dcc9ab2bf3248903e02d8da87e678977 + - path: results/reports/mosdepth/test/test.md.per-base.bed.gz + md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 + - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi + md5sum: b0ab630c3241fbd7581b7a38d944ff8b + - path: results/reports/mosdepth/test/test.md.regions.bed.gz + md5sum: 91e0d531f1bab64711ecefe52bfc8255 + - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi + md5sum: c6d1ac97ef4dfe43731c8368d8391cab + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 0b3162def977123809598639f7698121 + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: a8455eb2947de529abfa62b303986e0f + - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz + md5sum: d9fa560ff78ae106cfee9db2c90801b5 + - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi + md5sum: 4816eeb9af254ca40177b08cf11b98d2 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: 91e0d531f1bab64711ecefe52bfc8255 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: c6d1ac97ef4dfe43731c8368d8391cab + - path: results/reports/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/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary + md5sum: 43d53e36cbb1091f915b2499e545b41e + - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count + md5sum: 650f3dc78c5aaaecfe8ffa3d499e812f + - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.qual + contains: ["0 0 0 -nan 82 29 2.82759", "1.1 196 35 5.6 57 24 2.375", "3.16 205 38 5.39474 49 20 2.45"] + - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/freebayes + should_exist: false +- name: Run variant calling on germline sample with freebayes without intervals + command: nextflow run main.nf -profile test --tools freebayes --no_intervals + tags: + - freebayes + - germline + - no_intervals + - variant_calling + files: + - path: results/csv/markduplicates.csv + md5sum: 0d6120bb99e92f6810343270711ca53e + - path: results/csv/markduplicates_no_table.csv + md5sum: 2a2d3d4842befd4def39156463859ee3 + - path: results/csv/recalibrated.csv + md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 + - path: results/csv/variantcalled.csv + md5sum: 0cc6a67fedb2ef9ce97e463d310f9f30 + - 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/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: 4ac774bf5f1157e77426fd82f5ac0fbe + - 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/bcftools/freebayes/test/test.freebayes.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/fastqc/test-test_L1 + - path: results/reports/markduplicates/test/test.md.cram.metrics + contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] + - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt + md5sum: 76fa71922a3f748e507c2364c531dfcb + - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt + md5sum: abc5df85e302b79985627888870882da + - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt + md5sum: d536456436eb275159b8c6af83213d80 + - path: results/reports/mosdepth/test/test.md.regions.bed.gz + md5sum: 38fe39894abe62e38f8ac214cba64f2b + - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi + md5sum: b1c2a861f64e20a94108a6de3b76c582 + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 76fa71922a3f748e507c2364c531dfcb + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: abc5df85e302b79985627888870882da + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: d536456436eb275159b8c6af83213d80 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: 38fe39894abe62e38f8ac214cba64f2b + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: b1c2a861f64e20a94108a6de3b76c582 + - 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/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary + md5sum: 76c5919541536c12b5c8a6094d6d78d5 + - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count + md5sum: 0a0464beef110bc0f3c5a35d022b528e + - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.qual + contains: ["0 0 0 -nan 325 86 3.77907", "27.5873 359 84 4.27381 39 13 3", "40.5188 368 87 4.22989 30 10 3"] + - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/freebayes + should_exist: false +- name: Run variant calling on somatic sample with freebayes + command: nextflow run main.nf -profile test,pair,targeted --tools freebayes + tags: + - freebayes + - somatic + - variant_calling + files: + - path: results/csv/markduplicates.csv + md5sum: e8e587ac25253ff7ab8f1cc66d410c98 + - path: results/csv/markduplicates_no_table.csv + md5sum: 617574c9b607e5daaf4ad56d48982247 + - path: results/csv/recalibrated.csv + md5sum: 008dff17e2a0d96ef9c1cae12fcab6ab + - path: results/csv/variantcalled.csv + md5sum: b31f56256a1cfa839a2ea7f7ba6c1c45 + - 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/markduplicates/test2/test2.md.cram + # binary changes md5sums on reruns. + - path: results/preprocessing/markduplicates/test2/test2.md.cram.crai + # binary changes md5sums on reruns. + - path: results/preprocessing/recal_table/test/test.recal.table + md5sum: c990e4f1b7dbd5a3a623882a54ae2bf2 + - path: results/preprocessing/recal_table/test2/test2.recal.table + md5sum: 00d6877d68d622d81e4d633c4e340e7e + - 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/preprocessing/recalibrated/test2/test2.recal.cram + # binary changes md5sums on reruns. + - path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai + # binary changes md5sums on reruns. + - path: results/reports/bcftools/freebayes/test/test.freebayes.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/bcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/fastqc/test-test_L1 + - path: results/reports/markduplicates/test/test.md.cram.metrics + contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] + - path: results/reports/markduplicates/test2/test2.md.cram.metrics + contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"] + - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt + md5sum: 5a0679057c530e5945c9c5a3a17312dc + - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt + md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 + - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt + md5sum: dcc9ab2bf3248903e02d8da87e678977 + - path: results/reports/mosdepth/test/test.md.per-base.bed.gz + md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 + - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi + md5sum: b0ab630c3241fbd7581b7a38d944ff8b + - path: results/reports/mosdepth/test/test.md.regions.bed.gz + md5sum: 91e0d531f1bab64711ecefe52bfc8255 + - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi + md5sum: c6d1ac97ef4dfe43731c8368d8391cab + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 0b3162def977123809598639f7698121 + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: a8455eb2947de529abfa62b303986e0f + - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz + md5sum: d9fa560ff78ae106cfee9db2c90801b5 + - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi + md5sum: 4816eeb9af254ca40177b08cf11b98d2 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: 91e0d531f1bab64711ecefe52bfc8255 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: c6d1ac97ef4dfe43731c8368d8391cab + - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt + md5sum: f25166c3a0051bb4d8c11a210278de6c + - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt + md5sum: 3211135329e4077bd9bf0ba488e14371 + - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt + md5sum: ce0eb6d33c6d0dc720fbc6d1811abef8 + - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz + md5sum: 55c160e8f3c8c7761524646426611f6b + - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz.csi + md5sum: 4205a09ede17cdbdaad45e3553f73105 + - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz + md5sum: 1dd426a45f967a9f37dcddcaea29a582 + - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi + md5sum: c6d1ac97ef4dfe43731c8368d8391cab + - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt + md5sum: a1ef7e662ce993da4668e804952014ce + - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt + md5sum: 3211135329e4077bd9bf0ba488e14371 + - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt + md5sum: 70ad653c0c98baeeaf5085f1209a7bdb + - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz + md5sum: 250a9f15a7d3f102435fa98adccf48a3 + - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz.csi + md5sum: 8072f447199c60f24b01eede8b557333 + - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz + md5sum: 1dd426a45f967a9f37dcddcaea29a582 + - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi + md5sum: c6d1ac97ef4dfe43731c8368d8391cab + - path: results/reports/samtools/test/test.md.cram.stats + # conda changes md5sums for test. + - path: results/reports/samtools/test/test.recal.cram.stats + # conda changes md5sums for test. + - path: results/reports/samtools/test2/test2.md.cram.stats + # conda changes md5sums for test. + - path: results/reports/samtools/test2/test2.recal.cram.stats + # conda changes md5sums for test. + - path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary + md5sum: 43d53e36cbb1091f915b2499e545b41e + - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count + md5sum: 650f3dc78c5aaaecfe8ffa3d499e812f + - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.qual + contains: ["0 0 0 -nan 82 29 2.82759", "1.1 196 35 5.6 57 24 2.375", "3.16 205 38 5.39474 49 20 2.45"] + - path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.FILTER.summary + md5sum: ac61b178a3e15efb861b34f16d80fb67 + - path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.TsTv.count + md5sum: d7c0e0afd59f87dc4685487c0d497575 + - path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.TsTv.qual + # the text-based file test2_vs_test.freebayes.TsTv.qual seemingly changes content on reruns! + - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/freebayes + should_exist: false +- name: Run variant calling on somatic sample with freebayes without intervals + command: nextflow run main.nf -profile test,pair,targeted --tools freebayes --no_intervals + tags: + - freebayes + - somatic + - no_intervals + - variant_calling + files: + - path: results/csv/markduplicates.csv + md5sum: e8e587ac25253ff7ab8f1cc66d410c98 + - path: results/csv/markduplicates_no_table.csv + md5sum: 617574c9b607e5daaf4ad56d48982247 + - path: results/csv/recalibrated.csv + md5sum: 008dff17e2a0d96ef9c1cae12fcab6ab + - path: results/csv/variantcalled.csv + md5sum: b31f56256a1cfa839a2ea7f7ba6c1c45 + - 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/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/markduplicates/test2/test2.md.cram + # binary changes md5sums on reruns. + - path: results/preprocessing/markduplicates/test2/test2.md.cram.crai + # binary changes md5sums on reruns. + - path: results/preprocessing/recal_table/test/test.recal.table + md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe + - path: results/preprocessing/recal_table/test2/test2.recal.table + md5sum: 0626cd4337eab79b38b5bc5c95e0c003 + - 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/preprocessing/recalibrated/test2/test2.recal.cram + # binary changes md5sums on reruns. + - path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai + # binary changes md5sums on reruns. + - path: results/reports/bcftools/freebayes/test/test.freebayes.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/bcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/fastqc/test-test_L1 + - path: results/reports/markduplicates/test/test.md.cram.metrics + contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] + - path: results/reports/markduplicates/test2/test2.md.cram.metrics + contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"] + - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt + md5sum: 5a0679057c530e5945c9c5a3a17312dc + - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt + md5sum: 0010c2396a3173c7cf4983abe2eb6a4c + - path: results/reports/mosdepth/test/test.md.per-base.bed.gz + md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 + - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi + md5sum: b0ab630c3241fbd7581b7a38d944ff8b + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 5a0679057c530e5945c9c5a3a17312dc + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: 0010c2396a3173c7cf4983abe2eb6a4c + - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz + md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 + - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi + md5sum: b0ab630c3241fbd7581b7a38d944ff8b + - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt + md5sum: f25166c3a0051bb4d8c11a210278de6c + - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt + md5sum: d5e4084de2ea2a0a7b60b2d71c804d4b + - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz + md5sum: 55c160e8f3c8c7761524646426611f6b + - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz.csi + md5sum: 4205a09ede17cdbdaad45e3553f73105 + - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt + md5sum: f25166c3a0051bb4d8c11a210278de6c + - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt + md5sum: d5e4084de2ea2a0a7b60b2d71c804d4b + - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz + md5sum: 55c160e8f3c8c7761524646426611f6b + - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz.csi + md5sum: 4205a09ede17cdbdaad45e3553f73105 + - path: results/reports/samtools/test/test.md.cram.stats + # conda changes md5sums for test. + - path: results/reports/samtools/test/test.recal.cram.stats + # conda changes md5sums for test. + - path: results/reports/samtools/test2/test2.md.cram.stats + # conda changes md5sums for test. + - path: results/reports/samtools/test2/test2.recal.cram.stats + # conda changes md5sums for test. + - path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary + md5sum: 76c5919541536c12b5c8a6094d6d78d5 + - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count + md5sum: 0a0464beef110bc0f3c5a35d022b528e + - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.qual + contains: ["0 0 0 -nan 325 86 3.77907", "68.8262 377 88 4.28409 20 10 2", "321.335 393 96 4.09375 4 2 2"] + - path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.FILTER.summary + md5sum: 59e9d340b588537655020147e6d93e29 + - path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.TsTv.count + md5sum: 61ad00bb8cd47592b0671fabe26cf8cd + - path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.TsTv.qual + # the text-based file test2_vs_test.freebayes.TsTv.qual seemingly changes content on reruns! + - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/freebayes + should_exist: false +# - name: Run variant calling on tumor_only sample with freebayes +# command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes +# tags: +# - freebayes +# - tumor_only +# - variant_calling +# files: +# - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz +# - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz.tbi +# - name: Run variant calling on tumor_only sample with freebayes without intervals +# command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes --no_intervals +# tags: +# - freebayes +# - no_intervals +# - tumor_only +# - variant_calling +# files: +# - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz +# - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz.tbi diff --git a/tests/test_save_output_bam.yml b/tests/test_gatk4_spark.yml similarity index 54% rename from tests/test_save_output_bam.yml rename to tests/test_gatk4_spark.yml index 615b27a67d..6b8e3a2f83 100644 --- a/tests/test_save_output_bam.yml +++ b/tests/test_gatk4_spark.yml @@ -1,56 +1,91 @@ -- name: Run save_output_as_bam - command: nextflow run main.nf -profile test --save_output_as_bam +- name: Run default pipeline with gatk4_spark + command: nextflow run main.nf -profile test,use_gatk_spark tags: + - gatk4_spark - preprocessing - - save_output_as_bam files: - path: results/csv/markduplicates.csv - md5sum: 8679570b8db1937ee574fec36b25d7bc + md5sum: 0d6120bb99e92f6810343270711ca53e - path: results/csv/markduplicates_no_table.csv - md5sum: 145154b6037e90448273fbe8e8dec5d3 + md5sum: 2a2d3d4842befd4def39156463859ee3 - path: results/csv/recalibrated.csv - md5sum: 3ddc20eb105fdcc483945afd7d7d238c + md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 - path: results/multiqc - - path: results/preprocessing/markduplicates/test/test.md.bam.bai - md5sum: 3add495a02547bd9e6882935d2f3e1f7 - - path: results/preprocessing/markduplicates/test/test.md.bam - md5sum: ebb72f603f016ce37964259c61625360 + - path: results/preprocessing/markduplicates/test/test.md.cram + md5sum: cf0ebfe288ee7164cd2fcd028bda1887 + - path: results/preprocessing/markduplicates/test/test.md.cram.crai + md5sum: 2136b37eca3e806c77c39ee823231679 - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe - - path: results/preprocessing/recalibrated/test/test.recal.bam - # binary changes md5sums on reruns. - - path: results/preprocessing/recalibrated/test/test.recal.bam.bai - # binary changes md5sums on reruns. + md5sum: 5b6e5078b4a90f6cb982fa0f0df616c2 + - path: results/preprocessing/recalibrated/test/test.recal.cram + md5sum: 1c168110f006bacba2ed8783bb5a3dee + - path: results/preprocessing/recalibrated/test/test.recal.cram.crai + md5sum: 1c91543c9f75bc354274b1a1da745ee3 - path: results/reports/fastqc/test-test_L1 - path: results/reports/markduplicates/test/test.md.cram.metrics - contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] + # The text-based output-file test.md.cram.metrics only contains comments and no metrics, which is a bit odd. + # The file test.md.cram.metrics contains a timestamp which means that it cannot be tested using the md5sum. - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 76fa71922a3f748e507c2364c531dfcb + md5sum: 9269e959d5eec5273307693c6274f53e - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: abc5df85e302b79985627888870882da + md5sum: deb2df4f3ca19f441f0a22f04dea8723 - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: d536456436eb275159b8c6af83213d80 + md5sum: 96acf3439477a1448b7e1b43c020c7d0 - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 38fe39894abe62e38f8ac214cba64f2b + md5sum: c259a9fd73f576626c3a29841c2dc019 - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: b1c2a861f64e20a94108a6de3b76c582 + md5sum: cf85ba4692f016af70db2a594d9effdf - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 76fa71922a3f748e507c2364c531dfcb + md5sum: 9269e959d5eec5273307693c6274f53e - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: abc5df85e302b79985627888870882da + md5sum: deb2df4f3ca19f441f0a22f04dea8723 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: d536456436eb275159b8c6af83213d80 + md5sum: 96acf3439477a1448b7e1b43c020c7d0 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 38fe39894abe62e38f8ac214cba64f2b - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b1c2a861f64e20a94108a6de3b76c582 + md5sum: c259a9fd73f576626c3a29841c2dc019 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 52411f93d9b5382342b40a351c2e313c + # conda changes md5sums for test. - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 811d834ff8849e69e7c5925dc2a34257 + # conda changes md5sums for test. + - path: results/preprocessing/mapped/ + should_exist: false +- name: Run default pipeline with gatk4_spark & skipping all QC steps + command: nextflow run main.nf -profile test,use_gatk_spark --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools + tags: + - gatk4_spark + - preprocessing + - skip_qc + files: + - path: results/csv/markduplicates.csv + md5sum: 0d6120bb99e92f6810343270711ca53e + - path: results/csv/markduplicates_no_table.csv + md5sum: 2a2d3d4842befd4def39156463859ee3 + - path: results/csv/recalibrated.csv + md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 + - path: results/preprocessing/markduplicates/test/test.md.cram + md5sum: cf0ebfe288ee7164cd2fcd028bda1887 + - path: results/preprocessing/markduplicates/test/test.md.cram.crai + md5sum: 2136b37eca3e806c77c39ee823231679 + - path: results/preprocessing/recal_table/test/test.recal.table + md5sum: 5b6e5078b4a90f6cb982fa0f0df616c2 + - path: results/preprocessing/recalibrated/test/test.recal.cram + md5sum: 1c168110f006bacba2ed8783bb5a3dee + - path: results/preprocessing/recalibrated/test/test.recal.cram.crai + md5sum: 1c91543c9f75bc354274b1a1da745ee3 + - path: results/multiqc + should_exist: false + - path: results/reports/fastqc + should_exist: false + - path: results/reports/markduplicates + should_exist: false + - path: results/reports/mosdepth + should_exist: false + - path: results/reports/samtools + should_exist: false - name: Run save_output_as_bam with gatk4 spark command: nextflow run main.nf -profile test,use_gatk_spark --save_output_as_bam tags: + - gatk4_spark - preprocessing - save_output_as_bam files: @@ -62,9 +97,9 @@ md5sum: 3ddc20eb105fdcc483945afd7d7d238c - path: results/multiqc - path: results/preprocessing/markduplicates/test/test.md.bam - md5sum: 8bfd111af60ca7e63b233e59b0fb570b + # conda changes md5sums for test. - path: results/preprocessing/markduplicates/test/test.md.bam.bai - md5sum: fe8bc8655aff0d1a8093680390d98fab + # conda changes md5sums for test. - path: results/preprocessing/recal_table/test/test.recal.table md5sum: 5b6e5078b4a90f6cb982fa0f0df616c2 - path: results/preprocessing/recalibrated/test/test.recal.bam @@ -96,6 +131,6 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: cf85ba4692f016af70db2a594d9effdf - path: results/reports/samtools/test/test.md.cram.stats - md5sum: b573b2e930c5f68e7e4910faf9e51e44 + # conda changes md5sums for test. - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: a75731dca9b42d87d9997ea44aaf82fc + # conda changes md5sums for test. diff --git a/tests/test_gatk_spark.yml b/tests/test_gatk_spark.yml deleted file mode 100644 index e679023427..0000000000 --- a/tests/test_gatk_spark.yml +++ /dev/null @@ -1,52 +0,0 @@ -- name: Run default pipeline with gatk_spark - command: nextflow run main.nf -profile test,use_gatk_spark - tags: - - gatk4 - - gatk4_spark - - preprocessing - files: - - path: results/csv/markduplicates.csv - md5sum: 0d6120bb99e92f6810343270711ca53e - - path: results/csv/markduplicates_no_table.csv - md5sum: 2a2d3d4842befd4def39156463859ee3 - - path: results/csv/recalibrated.csv - md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 - - path: results/multiqc - - path: results/preprocessing/markduplicates/test/test.md.cram - md5sum: cf0ebfe288ee7164cd2fcd028bda1887 - - path: results/preprocessing/markduplicates/test/test.md.cram.crai - md5sum: 2136b37eca3e806c77c39ee823231679 - - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 5b6e5078b4a90f6cb982fa0f0df616c2 - - path: results/preprocessing/recalibrated/test/test.recal.cram - md5sum: 1c168110f006bacba2ed8783bb5a3dee - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - md5sum: 1c91543c9f75bc354274b1a1da745ee3 - - path: results/reports/fastqc/test-test_L1 - - path: results/reports/markduplicates/test/test.md.cram.metrics - # The text-based output-file test.md.cram.metrics only contains comments and no metrics, which is a bit odd. - # The file test.md.cram.metrics contains a timestamp which means that it cannot be tested using the md5sum. - - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 9269e959d5eec5273307693c6274f53e - - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: deb2df4f3ca19f441f0a22f04dea8723 - - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 96acf3439477a1448b7e1b43c020c7d0 - - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: c259a9fd73f576626c3a29841c2dc019 - - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: cf85ba4692f016af70db2a594d9effdf - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 9269e959d5eec5273307693c6274f53e - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: deb2df4f3ca19f441f0a22f04dea8723 - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 96acf3439477a1448b7e1b43c020c7d0 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: c259a9fd73f576626c3a29841c2dc019 - - path: results/reports/samtools/test/test.md.cram.stats - md5sum: b573b2e930c5f68e7e4910faf9e51e44 - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: a75731dca9b42d87d9997ea44aaf82fc - - path: results/preprocessing/mapped/ - should_exist: false diff --git a/tests/test_haplotypecaller.yml b/tests/test_haplotypecaller.yml new file mode 100644 index 0000000000..0d13eb3650 --- /dev/null +++ b/tests/test_haplotypecaller.yml @@ -0,0 +1,107 @@ +- name: Run variant calling on germline sample with haplotypecaller + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling + tags: + - germline + - haplotypecaller + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: d7d86e82902a4f57876b2414a4f812a4 + - 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 + should_exist: false + - path: results/preprocessing/recalibrated/test/test.recal.cram.crai + should_exist: false + - path: results/reports/bcftools/haplotypecaller/test/test.haplotypecaller.filtered.bcftools_stats.txt + md5sum: f9cc3809106a42601eafd3b09900750a + - path: results/reports/vcftools/haplotypecaller/test/test.haplotypecaller.filtered.FILTER.summary + md5sum: 4e2ceea7f3ff998004691fd71192d9ee + - path: results/reports/vcftools/haplotypecaller/test/test.haplotypecaller.filtered.TsTv.count + md5sum: b77c120ee5cc0423267200c67d60c663 + - path: results/reports/vcftools/haplotypecaller/test/test.haplotypecaller.filtered.TsTv.qual + md5sum: 1e34357e5848c318f8c2c7d3b041d229 + - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/haplotypecaller + should_exist: false +- name: Run variant calling on germline sample with haplotypecaller without intervals + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --no_intervals + tags: + - germline + - haplotypecaller + - no_intervals + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: d7d86e82902a4f57876b2414a4f812a4 + - 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/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 + should_exist: false + - path: results/preprocessing/recalibrated/test/test.recal.cram.crai + should_exist: false + - path: results/reports/bcftools/haplotypecaller/test/test.haplotypecaller.filtered.bcftools_stats.txt + md5sum: f9cc3809106a42601eafd3b09900750a + - path: results/reports/vcftools/haplotypecaller/test/test.haplotypecaller.filtered.FILTER.summary + md5sum: 4e2ceea7f3ff998004691fd71192d9ee + - path: results/reports/vcftools/haplotypecaller/test/test.haplotypecaller.filtered.TsTv.count + md5sum: b77c120ee5cc0423267200c67d60c663 + - path: results/reports/vcftools/haplotypecaller/test/test.haplotypecaller.filtered.TsTv.qual + md5sum: 1e34357e5848c318f8c2c7d3b041d229 + - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/haplotypecaller + should_exist: false +- name: Run joint germline variant calling with haplotypecaller + command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --joint_germline true --step variant_calling + tags: + - germline + - haplotypecaller + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: d2dffdbd2b4f1f26a06637592d24dab3 + - path: results/multiqc + - 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/bcftools/haplotypecaller/joint_variant_calling/joint_germline.bcftools_stats.txt + md5sum: f91f185319e00108870911e0ce1a7ed6 + - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.FILTER.summary + md5sum: 2a4eb7abfb2e64e45d53fdda17530b7f + - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.count + md5sum: 949fa16c755189c23a37f0ea8ecd1b26 + - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.qual + md5sum: 3b3a249fbc26c80ce0acbe91147291ea + - path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/haplotypecaller + should_exist: false diff --git a/tests/test_intervals.yml b/tests/test_intervals.yml index 9d1d528623..457e46938e 100644 --- a/tests/test_intervals.yml +++ b/tests/test_intervals.yml @@ -1,5 +1,64 @@ +- name: Run default pipeline with target bed + command: nextflow run main.nf -profile test,targeted + tags: + - intervals + - preprocessing + - targeted + files: + - path: results/csv/markduplicates.csv + md5sum: 0d6120bb99e92f6810343270711ca53e + - path: results/csv/markduplicates_no_table.csv + md5sum: 2a2d3d4842befd4def39156463859ee3 + - path: results/csv/recalibrated.csv + md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 + - 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: c990e4f1b7dbd5a3a623882a54ae2bf2 + - 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/fastqc/test-test_L1 + - path: results/reports/markduplicates/test/test.md.cram.metrics + contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] + - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt + md5sum: 5a0679057c530e5945c9c5a3a17312dc + - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt + md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 + - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt + md5sum: dcc9ab2bf3248903e02d8da87e678977 + - path: results/reports/mosdepth/test/test.md.per-base.bed.gz + md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 + - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi + md5sum: b0ab630c3241fbd7581b7a38d944ff8b + - path: results/reports/mosdepth/test/test.md.regions.bed.gz + md5sum: 91e0d531f1bab64711ecefe52bfc8255 + - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi + md5sum: c6d1ac97ef4dfe43731c8368d8391cab + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 0b3162def977123809598639f7698121 + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: a8455eb2947de529abfa62b303986e0f + - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz + md5sum: d9fa560ff78ae106cfee9db2c90801b5 + - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi + md5sum: 4816eeb9af254ca40177b08cf11b98d2 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: 91e0d531f1bab64711ecefe52bfc8255 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: c6d1ac97ef4dfe43731c8368d8391cab + - path: results/reports/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 intervals false pipeline - command: nextflow run main.nf -profile test --intervals false + command: nextflow run main.nf -profile test --intervals false --save_reference tags: - intervals - intervals_false @@ -22,6 +81,10 @@ # binary changes md5sums on reruns. - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns. + - path: results/reference/intervals/chr22_1-40001.bed + md5sum: 87a15eb9c2ff20ccd5cd8735a28708f7 + - path: results/reference/intervals/chr22_1-40001.bed.gz + md5sum: d3341fa28986c40b24fcc10a079dbb80 - path: results/reports/fastqc/test-test_L1 - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] @@ -42,10 +105,9 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz md5sum: 38fe39894abe62e38f8ac214cba64f2b - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 52411f93d9b5382342b40a351c2e313c + # conda changes md5sums for test. - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 811d834ff8849e69e7c5925dc2a34257 - + # conda changes md5sums for test. - name: Run default pipeline without intervals command: nextflow run main.nf -profile test,no_intervals tags: @@ -76,6 +138,8 @@ # binary changes md5sums on reruns. - path: results/preprocessing/recalibrated/test/test.recal.cram.crai # binary changes md5sums on reruns. + - path: results/reference/intervals + should_exist: false - path: results/reports/fastqc/test-test_L1 - path: results/reports/markduplicates/test/test.md.cram.metrics contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] @@ -100,6 +164,6 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi md5sum: b1c2a861f64e20a94108a6de3b76c582 - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 52411f93d9b5382342b40a351c2e313c + # conda changes md5sums for test. - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: d80ad11b8e308a3d5b1fb6f8e13cef38 + # conda changes md5sums for test. diff --git a/tests/test_manta.yml b/tests/test_manta.yml new file mode 100644 index 0000000000..64957769db --- /dev/null +++ b/tests/test_manta.yml @@ -0,0 +1,213 @@ +- name: Run variant calling on germline sample with manta + command: nextflow run main.nf -profile test,tools_germline --tools manta + tags: + - germline + - manta + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: 981280af86f69190fdf0639030a80249 + - path: results/multiqc + - path: results/reports/bcftools/manta/sample1/sample1.manta.diploid_sv.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/vcftools/manta/sample1/sample1.manta.diploid_sv.FILTER.summary + md5sum: 1ce42d34e4ae919afb519efc99146423 + - path: results/reports/vcftools/manta/sample1/sample1.manta.diploid_sv.TsTv.count + md5sum: fa27f678965b7cba6a92efcd039f802a + - path: results/reports/vcftools/manta/sample1/sample1.manta.diploid_sv.TsTv.qual + md5sum: bc68ae4e688e9fb772b457069e604883 + - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/manta + should_exist: false +- name: Run variant calling on germline sample with manta without intervals + command: nextflow run main.nf -profile test,tools_germline --tools manta --no_intervals + tags: + - germline + - manta + - no_intervals + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: 981280af86f69190fdf0639030a80249 + - 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/sample1/sample1.manta.diploid_sv.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/vcftools/manta/sample1/sample1.manta.diploid_sv.FILTER.summary + md5sum: 1ce42d34e4ae919afb519efc99146423 + - path: results/reports/vcftools/manta/sample1/sample1.manta.diploid_sv.TsTv.count + md5sum: fa27f678965b7cba6a92efcd039f802a + - path: results/reports/vcftools/manta/sample1/sample1.manta.diploid_sv.TsTv.qual + md5sum: bc68ae4e688e9fb772b457069e604883 + - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz.tbi + md5sum: 4cb176febbc8c26d717a6c6e67b9c905 + - path: results/manta + should_exist: false +- name: Run variant calling on tumor_only sample with manta + command: nextflow run main.nf -profile test,tools_tumoronly --tools manta + tags: + - manta + - tumor_only + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: f1051fe647abf202e6332f9a1789c05d + - path: results/multiqc + - path: results/reports/bcftools/manta/sample2/sample2.manta.tumor_sv.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/vcftools/manta/sample2/sample2.manta.tumor_sv.FILTER.summary + md5sum: 1ce42d34e4ae919afb519efc99146423 + - path: results/reports/vcftools/manta/sample2/sample2.manta.tumor_sv.TsTv.count + md5sum: fa27f678965b7cba6a92efcd039f802a + - path: results/reports/vcftools/manta/sample2/sample2.manta.tumor_sv.TsTv.qual + md5sum: bc68ae4e688e9fb772b457069e604883 + - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz.tbi + md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4 + - path: results/manta + should_exist: false +- name: Run variant calling on tumor_only sample with manta without intervals + command: nextflow run main.nf -profile test,tools_tumoronly --tools manta --no_intervals + tags: + - manta + - no_intervals + - tumor_only + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: f1051fe647abf202e6332f9a1789c05d + - 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/sample2/sample2.manta.tumor_sv.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/vcftools/manta/sample2/sample2.manta.tumor_sv.FILTER.summary + md5sum: 1ce42d34e4ae919afb519efc99146423 + - path: results/reports/vcftools/manta/sample2/sample2.manta.tumor_sv.TsTv.count + md5sum: fa27f678965b7cba6a92efcd039f802a + - path: results/reports/vcftools/manta/sample2/sample2.manta.tumor_sv.TsTv.qual + md5sum: bc68ae4e688e9fb772b457069e604883 + - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz.tbi + md5sum: 4cb176febbc8c26d717a6c6e67b9c905 + - path: results/manta + should_exist: false +- name: Run variant calling on somatic sample with manta + command: nextflow run main.nf -profile test,tools_somatic --tools manta + tags: + - manta + - somatic + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: 3a8861808601994f89d5c55ce5c95dae + - 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/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 + md5sum: bc68ae4e688e9fb772b457069e604883 + - 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 + md5sum: bc68ae4e688e9fb772b457069e604883 + - 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 + md5sum: bc68ae4e688e9fb772b457069e604883 + - 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: e7ca7e9fe76ce12198fd54ec9a64fad4 + - 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: e7ca7e9fe76ce12198fd54ec9a64fad4 + - 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: e7ca7e9fe76ce12198fd54ec9a64fad4 + - path: results/manta + should_exist: false +- name: Run variant calling on somatic sample with manta without intervals + command: nextflow run main.nf -profile test,tools_somatic --tools manta --no_intervals + tags: + - manta + - no_intervals + - somatic + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: 3a8861808601994f89d5c55ce5c95dae + - 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/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 + md5sum: bc68ae4e688e9fb772b457069e604883 + - 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 + md5sum: bc68ae4e688e9fb772b457069e604883 + - 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 + md5sum: bc68ae4e688e9fb772b457069e604883 + - 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/manta + should_exist: false diff --git a/tests/test_markduplicates.yml b/tests/test_markduplicates_from_bam.yml similarity index 68% rename from tests/test_markduplicates.yml rename to tests/test_markduplicates_from_bam.yml index 259203f354..d10b1f9354 100644 --- a/tests/test_markduplicates.yml +++ b/tests/test_markduplicates_from_bam.yml @@ -1,7 +1,7 @@ - name: Run markduplicates starting from BAM command: nextflow run main.nf -profile test,markduplicates_bam tags: - - bam + - input_bam - markduplicates - preprocessing files: @@ -49,58 +49,59 @@ - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi # binary changes md5sums on reruns. - path: results/reports/samtools/test/test.md.cram.stats - md5sum: a0ecedb6be28639e276d38e4ac18935b + # conda changes md5sums for test. - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 69d2bab6fdbe21ec5c598dc404a3df00 -- name: Run markduplicates starting from CRAM - command: nextflow run main.nf -profile test,markduplicates_cram + # conda changes md5sums for test. +- name: Run skip markduplicates bam from step markduplicates + command: nextflow run main.nf -profile test,markduplicates_bam,skip_markduplicates tags: - - cram + - input_bam - markduplicates - preprocessing + - skip_markduplicates 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 + - 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.py - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf + 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/markduplicates/test/test.md.cram.metrics - contains: ["testN 0 2820 2 2 0 828 0 0.293617 3807", "1.0 0.999986 1178 1178", "100.0 1.911145 0 0"] - - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 - - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d - - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 - - path: results/reports/mosdepth/test/test.md.regions.bed.gz - # binary changes md5sums on reruns. - - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - # binary changes md5sums on reruns. - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 + md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 75e1ce7e55af51f4985fa91654a5ea2d + md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: b23cf96942b2ada3f41172a9349a1175 + md5sum: 32ea70ef1b99def3dc900b4afd513a40 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - # binary changes md5sums on reruns. + md5sum: d034a60ae5c0768d67b9ba6442bd2212 - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - # binary changes md5sums on reruns. - - path: results/reports/samtools/test/test.md.cram.stats - md5sum: a0ecedb6be28639e276d38e4ac18935b + md5sum: b3716e5cd1744610e69c29bd4ffad259 + - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt + md5sum: bdb8f185c35dd1eec7ce2f69bce57972 + - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt + md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt + md5sum: 32ea70ef1b99def3dc900b4afd513a40 + - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz + md5sum: d034a60ae5c0768d67b9ba6442bd2212 + - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi + md5sum: b3716e5cd1744610e69c29bd4ffad259 - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 69d2bab6fdbe21ec5c598dc404a3df00 - - path: results/preprocessing/mapped/ + # 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 new file mode 100644 index 0000000000..1accab1b5e --- /dev/null +++ b/tests/test_markduplicates_from_cram.yml @@ -0,0 +1,101 @@ +- name: Run markduplicates starting from CRAM + command: nextflow run main.nf -profile test,markduplicates_cram + tags: + - input_cram + - 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 + md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 + - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt + md5sum: 75e1ce7e55af51f4985fa91654a5ea2d + - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt + md5sum: b23cf96942b2ada3f41172a9349a1175 + - path: results/reports/mosdepth/test/test.md.regions.bed.gz + # binary changes md5sums on reruns. + - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi + # binary changes md5sums on reruns. + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: 8e875e20e3fb9cf288d68c1d223f6fd5 + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: 75e1ce7e55af51f4985fa91654a5ea2d + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: b23cf96942b2ada3f41172a9349a1175 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + # binary changes md5sums on reruns. + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + # binary changes md5sums on reruns. + - path: results/reports/samtools/test/test.md.cram.stats + # conda changes md5sums for test. + - path: results/reports/samtools/test/test.recal.cram.stats + # 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 + 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 + md5sum: adac39d7845f64f6b35b766751393b06 + - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt + md5sum: bdb8f185c35dd1eec7ce2f69bce57972 + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: 32ea70ef1b99def3dc900b4afd513a40 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: d034a60ae5c0768d67b9ba6442bd2212 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: b3716e5cd1744610e69c29bd4ffad259 + - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt + md5sum: bdb8f185c35dd1eec7ce2f69bce57972 + - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt + md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt + md5sum: 32ea70ef1b99def3dc900b4afd513a40 + - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz + md5sum: d034a60ae5c0768d67b9ba6442bd2212 + - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi + md5sum: b3716e5cd1744610e69c29bd4ffad259 + - 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_mpileup.yml b/tests/test_mpileup.yml new file mode 100644 index 0000000000..3ace5ecf32 --- /dev/null +++ b/tests/test_mpileup.yml @@ -0,0 +1,58 @@ +- name: Run variant calling on tumor_only sample to test mpileup + command: nextflow run main.nf -profile test,tools_tumoronly --tools mpileup + tags: + - tumor_only + - mpileup + files: + - path: results/multiqc + - path: results/variant_calling/mpileup/sample2/sample2.tumor.mpileup.gz + # binary changes md5sums on reruns. + - path: results/mpileup + should_exist: false +- name: Run variant calling on tumor_only sample to test mpileup without intervals + command: nextflow run main.nf -profile test,tools_tumoronly --tools mpileup --no_intervals + tags: + - tumor_only + - mpileup + - no_intervals + files: + - 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/variant_calling/mpileup/sample2/sample2.tumor.mpileup.gz + # binary changes md5sums on reruns. + - path: results/mpileup + should_exist: false +- name: Run variant calling on germline sample to test mpileup + command: nextflow run main.nf -profile test,tools_germline --tools mpileup + tags: + - germline + - mpileup + files: + - path: results/multiqc + - path: results/variant_calling/mpileup/sample1/sample1.normal.mpileup.gz + # binary changes md5sums on reruns. + - path: results/mpileup + should_exist: false +- name: Run variant calling on germline sample to test mpileup without intervals + command: nextflow run main.nf -profile test,tools_germline --tools mpileup --no_intervals + tags: + - germline + - mpileup + - no_intervals + files: + - 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/variant_calling/mpileup/sample1/sample1.normal.mpileup.gz + # binary changes md5sums on reruns. + - path: results/mpileup + should_exist: false diff --git a/tests/test_msisensorpro.yml b/tests/test_msisensorpro.yml new file mode 100644 index 0000000000..6d2de98243 --- /dev/null +++ b/tests/test_msisensorpro.yml @@ -0,0 +1,14 @@ +- name: Run variant calling on somatic sample with msisensor-pro + command: nextflow run main.nf -profile test,tools_somatic --tools msisensorpro + tags: + - msisensorpro + - somatic + - variant_calling + files: + - path: results/multiqc + - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3 + - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3_dis + - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3_germline + - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3_somatic + - path: results/msisensorpro + should_exist: false diff --git a/tests/test_mutect2.yml b/tests/test_mutect2.yml new file mode 100644 index 0000000000..22340a34c5 --- /dev/null +++ b/tests/test_mutect2.yml @@ -0,0 +1,87 @@ +- name: Run variant calling on tumor only sample with mutect2 + command: nextflow run main.nf -profile test,tools_tumoronly --tools mutect2 + tags: + - mutect2 + - tumor_only + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: d57c1beba9005e9790a573bd93398b72 + - path: results/multiqc + - path: results/reports/bcftools/mutect2/sample2/sample2.mutect2.filtered.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/vcftools/mutect2/sample2/sample2.mutect2.filtered.FILTER.summary + md5sum: ef9bd9a2f41d8872ba25e5616e4c2a5e + - path: results/reports/vcftools/mutect2/sample2/sample2.mutect2.filtered.TsTv.count + md5sum: fe3ff1f0c2ead72f037552727438e00a + - path: results/reports/vcftools/mutect2/sample2/sample2.mutect2.filtered.TsTv.qual + # conda changes md5sums for test. + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.artifactprior.tar.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.contamination.table + md5sum: 46c708c943b453da89a3da08acfdb2a7 + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz.filteringStats.tsv + md5sum: 9a8439d0bb5875f1e673cf592af85ffb + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.pileupsummaries.table + md5sum: 9afe42339f590937166edcf4746c22ec + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.segmentation.table + md5sum: f4643d9319bde4efbfbe516d6fb13052 + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.stats + md5sum: 3cc40a35727af6c5223fb45678f3f172 + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/mutect2 + should_exist: false +- name: Run variant calling on tumor only sample with mutect2 without intervals + command: nextflow run main.nf -profile test,tools_tumoronly --tools mutect2 --no_intervals + tags: + - mutect2 + - no_intervals + - tumor_only + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: d57c1beba9005e9790a573bd93398b72 + - 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/mutect2/sample2/sample2.mutect2.filtered.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/vcftools/mutect2/sample2/sample2.mutect2.filtered.FILTER.summary + md5sum: 5a833fd50e6efb26d1df2336eb0caf5e + - path: results/reports/vcftools/mutect2/sample2/sample2.mutect2.filtered.TsTv.count + md5sum: f5295a61da80f12babae74fe4e104aad + - path: results/reports/vcftools/mutect2/sample2/sample2.mutect2.filtered.TsTv.qual + # conda changes md5sums for test. + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.artifactprior.tar.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.contamination.table + md5sum: 46c708c943b453da89a3da08acfdb2a7 + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz.filteringStats.tsv + md5sum: e4eac0c602dd25aa61a6dc26a2b61844 + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.pileupsummaries.table + md5sum: fe35b6bc041f2df8bd1f23420af3ddf9 + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.segmentation.table + md5sum: f4643d9319bde4efbfbe516d6fb13052 + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz + # binary changes md5sums on reruns. + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.stats + md5sum: 55ed641e16089afb33cdbc478e202d3d + - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.tbi + # binary changes md5sums on reruns. + - path: results/mutect2 + should_exist: false diff --git a/tests/test_only_paired_VC.yml b/tests/test_only_paired_VC.yml deleted file mode 100644 index b051b3e2b7..0000000000 --- a/tests/test_only_paired_VC.yml +++ /dev/null @@ -1,113 +0,0 @@ -- name: Run variant calling on somatic samples with cnvkit and skip variant calling on matched normal - command: nextflow run main.nf -profile test,tools_somatic --tools cnvkit --only_paired_variant_calling - tags: - - cnvkit - - somatic - - only_paired_variant_calling - - copy_number_calling - files: - - path: results/multiqc - - path: results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.antitarget.bed - md5sum: 3d4d20f9f23b39970865d29ef239d20b - - path: results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.target.bed - md5sum: 86d30493bb2e619a93f4ebc2923d29f3 - - path: results/variant_calling/cnvkit/sample4_vs_sample3/reference.cnn - md5sum: 59ec306bb820684b1f6f277d67cb2d92 - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn - md5sum: fe1248aa91fad7769303bb4c031d55ca - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test.paired_end.recalibrated.sorted.targetcoverage.cnn - md5sum: 79aae7e9c135fb8c65f8fbda12610faf - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted-diagram.pdf - # binary changes md5sums on reruns. - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted-scatter.png - md5sum: acd87dfb61db5910afaea34053aed561 - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn - md5sum: 067115082c4af4b64d58c0dc3a3642e4 - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.bintest.cns - md5sum: e9a260b81a34d8bc75330435d2a5e8da - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.call.cns - md5sum: c7d7fd87b27e103f73988ae307450e82 - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cnr - md5sum: 26c506866198d46610c71fa6c0f9e381 - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cns - md5sum: 83510b274c24a2671a962477a1ceb436 - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn - md5sum: b4a49faf170e436ec32dcc21ccc3ce8f -- name: Skip variant calling on matched normal - command: nextflow run main.nf -profile test,variantcalling_channels --tools strelka --only_paired_variant_calling - tags: - - somatic - - strelka - - variantcalling_channel - files: - - path: results/multiqc - - path: results/reports/bcftools/strelka/sample1/sample1.strelka.variants.bcftools_stats.txt - md5sum: fa17527ede69d65762bd78fe86fbe50a - - path: results/reports/bcftools/strelka/sample2/sample2.strelka.variants.bcftools_stats.txt - md5sum: 93bf8f09d155e69418fff988e76cbc1d - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt - md5sum: 6cf7a55bcb53b400ce7df7e72c892574 - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt - md5sum: 7cc6f2412d6b3d8e84ec0daece3d5443 - - 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 - md5sum: f01534408c3a87893b523de5f39deb0b - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: c949f848859f138731898aac64a73eaf - - 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 diff --git a/tests/test_pair.yml b/tests/test_pair.yml deleted file mode 100644 index 20cddcc05b..0000000000 --- a/tests/test_pair.yml +++ /dev/null @@ -1,89 +0,0 @@ -- name: Run default pipeline for tumor normal pair - command: nextflow run main.nf -profile test,pair - tags: - - preprocessing - - tumor_normal_pair - files: - - path: results/csv/markduplicates.csv - md5sum: e8e587ac25253ff7ab8f1cc66d410c98 - - path: results/csv/markduplicates_no_table.csv - md5sum: 617574c9b607e5daaf4ad56d48982247 - - path: results/csv/recalibrated.csv - md5sum: 008dff17e2a0d96ef9c1cae12fcab6ab - - 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: 4ac774bf5f1157e77426fd82f5ac0fbe - - 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/preprocessing/markduplicates/test2/test2.md.cram - # binary changes md5sums on reruns. - - path: results/preprocessing/markduplicates/test2/test2.md.cram.crai - # binary changes md5sums on reruns. - - path: results/preprocessing/recal_table/test2/test2.recal.table - md5sum: 0626cd4337eab79b38b5bc5c95e0c003 - - path: results/preprocessing/recalibrated/test2/test2.recal.cram - # binary changes md5sums on reruns. - - path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai - # binary changes md5sums on reruns. - - path: results/reports/fastqc/test-test_L1 - - path: results/reports/fastqc/test2-test_L1 - - path: results/reports/markduplicates/test/test.md.cram.metrics - contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] - - path: results/reports/markduplicates/test2/test2.md.cram.metrics - contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"] - - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 76fa71922a3f748e507c2364c531dfcb - - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: abc5df85e302b79985627888870882da - - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: d536456436eb275159b8c6af83213d80 - - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 38fe39894abe62e38f8ac214cba64f2b - - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: b1c2a861f64e20a94108a6de3b76c582 - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 76fa71922a3f748e507c2364c531dfcb - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: abc5df85e302b79985627888870882da - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: d536456436eb275159b8c6af83213d80 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 38fe39894abe62e38f8ac214cba64f2b - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b1c2a861f64e20a94108a6de3b76c582 - - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt - md5sum: 2020cf6dfc7ddca020c921dd9f0549b7 - - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt - md5sum: 38ff8b38c33b9231f047fea8ea830aae - - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt - md5sum: 8b991358768cade225470a07cd34f573 - - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz - md5sum: 5d67bc6ea9f077abb4fdac3b087c6387 - - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi - md5sum: d5f1c9389ecf52ba839e834780a94549 - - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt - md5sum: 2020cf6dfc7ddca020c921dd9f0549b7 - - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt - md5sum: 38ff8b38c33b9231f047fea8ea830aae - - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt - md5sum: 8b991358768cade225470a07cd34f573 - - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz - md5sum: 5d67bc6ea9f077abb4fdac3b087c6387 - - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi - md5sum: d5f1c9389ecf52ba839e834780a94549 - - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 52411f93d9b5382342b40a351c2e313c - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 811d834ff8849e69e7c5925dc2a34257 - - path: results/reports/samtools/test2/test2.md.cram.stats - md5sum: 60152dbf1e109d4c407c151204388109 - - path: results/reports/samtools/test2/test2.recal.cram.stats - md5sum: 2907543ab51cabd97318b15cf035c867 - - path: results/preprocessing/mapped/ - should_exist: false diff --git a/tests/test_prepare_recalibration.yml b/tests/test_prepare_recalibration.yml deleted file mode 100644 index a2d94d03aa..0000000000 --- a/tests/test_prepare_recalibration.yml +++ /dev/null @@ -1,168 +0,0 @@ -- name: Run prepare_recalibration starting from bam - command: nextflow run main.nf -profile test,prepare_recalibration_bam - tags: - - 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 - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 71af990f7acad8bf24d37e88c4adcded - - path: results/preprocessing/mapped/ - should_exist: false - - path: results/preprocessing/markduplicates/ - should_exist: false -- name: Run prepare_recalibration starting from cram - command: nextflow run main.nf -profile test,prepare_recalibration_cram - tags: - - 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 - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 71af990f7acad8bf24d37e88c4adcded - - 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 - tags: - - 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 - md5sum: 0741b5dd5e6c5428bd5d4f1b7a923dd5 - - 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 - md5sum: 9fe11e894f7567eb96b43c48593741a7 - - 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 -- name: Run prepare_recalibration starting from cram and skip baserecalibration - command: nextflow run main.nf -profile test,prepare_recalibration_cram,skip_bqsr --tools strelka - tags: - - 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 - md5sum: 0741b5dd5e6c5428bd5d4f1b7a923dd5 - - 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 - md5sum: a7e5db212d1e4d05029e93ff6e6b843a - - 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_prepare_recalibration_from_bam.yml b/tests/test_prepare_recalibration_from_bam.yml new file mode 100644 index 0000000000..6f12f71581 --- /dev/null +++ b/tests/test_prepare_recalibration_from_bam.yml @@ -0,0 +1,84 @@ +- name: Run prepare_recalibration starting from bam + command: nextflow run main.nf -profile test,prepare_recalibration_bam + 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 + md5sum: bdb8f185c35dd1eec7ce2f69bce57972 + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: 32ea70ef1b99def3dc900b4afd513a40 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: d034a60ae5c0768d67b9ba6442bd2212 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: b3716e5cd1744610e69c29bd4ffad259 + - path: results/reports/samtools/test/test.recal.cram.stats + # conda changes md5sums for test. + - path: results/preprocessing/mapped/ + 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 + 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 new file mode 100644 index 0000000000..22be04acf8 --- /dev/null +++ b/tests/test_prepare_recalibration_from_cram.yml @@ -0,0 +1,84 @@ +- name: Run prepare_recalibration starting from cram + command: nextflow run main.nf -profile test,prepare_recalibration_cram + 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 + md5sum: bdb8f185c35dd1eec7ce2f69bce57972 + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: 32ea70ef1b99def3dc900b4afd513a40 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: d034a60ae5c0768d67b9ba6442bd2212 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: b3716e5cd1744610e69c29bd4ffad259 + - path: results/reports/samtools/test/test.recal.cram.stats + # conda changes md5sums for test. + - path: results/preprocessing/mapped/ + 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 + 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.yml b/tests/test_recalibrate.yml deleted file mode 100644 index e64114cbbf..0000000000 --- a/tests/test_recalibrate.yml +++ /dev/null @@ -1,178 +0,0 @@ -- name: Run Recalibration starting from bam - command: nextflow run main.nf -profile test,recalibrate_bam - tags: - - 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 - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: a0841c41460d0d4bdc2a1a777ee7e7c2 - - path: results/preprocessing/mapped/ - should_exist: false - - path: results/preprocessing/markduplicates/ - should_exist: false -- name: Run Recalibration starting from cram - command: nextflow run main.nf -profile test,recalibrate_cram - tags: - - 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 - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: a0841c41460d0d4bdc2a1a777ee7e7c2 - - 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 - tags: - - bam - - recalibrate - - preprocessing - - variant_calling - - strelka - 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 - md5sum: 0741b5dd5e6c5428bd5d4f1b7a923dd5 - - 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 - # The text-based file test.strelka.variants.TsTv.qual has different md5sums on my linux system and the GitHub-test-server. - # I don't know exactly why that is, but it file contains some very small numbers written in scientific notation 4.00193e-322 which might change slightly on different systems. - # Instead I'll try some string testing - 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 -- name: Run Recalibration starting from cram and skip baserecalibration - command: nextflow run main.nf -profile test,recalibrate_cram,skip_bqsr --tools strelka - tags: - - cram - - recalibrate - - preprocessing - - variant_calling - - strelka - files: - - path: results/csv/variantcalled.csv - md5sum: 4d0effd3d8dc2b814230a189e7ca9dba - - path: results/multiqc - - path: results/reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt - md5sum: 0741b5dd5e6c5428bd5d4f1b7a923dd5 - - 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 - # The text-based file test.strelka.variants.TsTv.qual has different md5sums on my linux system and the GitHub-test-server. - # I don't know exactly why that is, but it file contains some very small numbers written in scientific notation 4.00193e-322 which might change slightly on different systems. - # Instead I'll try some string testing - 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_recalibrate_from_bam.yml b/tests/test_recalibrate_from_bam.yml new file mode 100644 index 0000000000..a4e92a8792 --- /dev/null +++ b/tests/test_recalibrate_from_bam.yml @@ -0,0 +1,90 @@ +- name: Run Recalibration starting from bam + command: nextflow run main.nf -profile test,recalibrate_bam + 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 + md5sum: bdb8f185c35dd1eec7ce2f69bce57972 + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: 32ea70ef1b99def3dc900b4afd513a40 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: d034a60ae5c0768d67b9ba6442bd2212 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: b3716e5cd1744610e69c29bd4ffad259 + - path: results/reports/samtools/test/test.recal.cram.stats + # conda changes md5sums for test. + - path: results/preprocessing/mapped/ + 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 + 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 + # The text-based file test.strelka.variants.TsTv.qual has different md5sums on my linux system and the GitHub-test-server. + # I don't know exactly why that is, but it file contains some very small numbers written in scientific notation 4.00193e-322 which might change slightly on different systems. + # Instead I'll try some string testing + 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 new file mode 100644 index 0000000000..a30908cdca --- /dev/null +++ b/tests/test_recalibrate_from_cram.yml @@ -0,0 +1,86 @@ +- name: Run Recalibration starting from cram + command: nextflow run main.nf -profile test,recalibrate_cram + 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 + md5sum: bdb8f185c35dd1eec7ce2f69bce57972 + - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt + md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 + - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt + md5sum: 32ea70ef1b99def3dc900b4afd513a40 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz + md5sum: d034a60ae5c0768d67b9ba6442bd2212 + - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi + md5sum: b3716e5cd1744610e69c29bd4ffad259 + - path: results/reports/samtools/test/test.recal.cram.stats + # conda changes md5sums for test. + - path: results/preprocessing/mapped/ + 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 + 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 + # The text-based file test.strelka.variants.TsTv.qual has different md5sums on my linux system and the GitHub-test-server. + # I don't know exactly why that is, but it file contains some very small numbers written in scientific notation 4.00193e-322 which might change slightly on different systems. + # Instead I'll try some string testing + 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_skip_markduplicates.yml b/tests/test_skip_markduplicates.yml deleted file mode 100644 index 87bc3e0fcf..0000000000 --- a/tests/test_skip_markduplicates.yml +++ /dev/null @@ -1,258 +0,0 @@ -- name: Run default pipeline with skipping MarkDuplicates - command: nextflow run main.nf -profile test,skip_markduplicates - tags: - - preprocessing - - skip_markduplicates - files: - - path: results/csv/mapped.csv - md5sum: ae97b7394ab53a6b60921ab06c713cd9 - - path: results/csv/recalibrated.csv - md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 - - path: results/multiqc - - path: results/preprocessing/mapped/test/test.sorted.cram - # binary changes md5sums on reruns. - - path: results/preprocessing/mapped/test/test.sorted.cram.crai - # binary changes md5sums on reruns. - - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 8de213f4c00fac61a1102633760493df - - 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/fastqc/test-test_L1 - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 48aa760b024d7c0ddd5a66f89a1cb544 - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 71e938314bba70f978271b2b56cb7ad3 - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 0786d56af0672eaef44b29f4ed5c12cb - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: b8719430e56a58f734884bb422a7b8fa - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: e3235323f455414ee3acc7144e659caf - - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: 48aa760b024d7c0ddd5a66f89a1cb544 - - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 71e938314bba70f978271b2b56cb7ad3 - - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: 0786d56af0672eaef44b29f4ed5c12cb - - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: b8719430e56a58f734884bb422a7b8fa - - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: e3235323f455414ee3acc7144e659caf - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 55ddd2d98552a1483bf2a965f19d8da4 - - path: results/reports/samtools/test/test.sorted.cram.stats - md5sum: 59d921ed3970e19145fbae75966de3e3 - - 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 -- name: Run skip markduplicates bam from step markduplicates - command: nextflow run main.nf -profile test,markduplicates_bam,skip_markduplicates - tags: - - bam - - 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.py - - 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 - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 71af990f7acad8bf24d37e88c4adcded - - path: results/reports/samtools/test/test.sorted.cram.stats - md5sum: 9de0a2738ab150e2e3fd857b0f42efc4 - - 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 -- name: Run skip markduplicates cram from step markduplicates - command: nextflow run main.nf -profile test,markduplicates_cram,skip_markduplicates - tags: - - cram - - 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 - md5sum: adac39d7845f64f6b35b766751393b06 - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: bdb8f185c35dd1eec7ce2f69bce57972 - - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 6fd2e5c5c938bf69cdb2811f9e3afef8 - - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: 32ea70ef1b99def3dc900b4afd513a40 - - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: d034a60ae5c0768d67b9ba6442bd2212 - - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: b3716e5cd1744610e69c29bd4ffad259 - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 71af990f7acad8bf24d37e88c4adcded - - path: results/reports/samtools/test/test.sorted.cram.stats - md5sum: 42b536ada66f772bb4dfd741098b2783 - - 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 -- name: Run default pipeline with skipping MarkDuplicates with save_mapped - command: nextflow run main.nf -profile test,skip_markduplicates --save_mapped - tags: - - preprocessing - - skip_markduplicates - files: - - path: results/csv/mapped.csv - md5sum: ae97b7394ab53a6b60921ab06c713cd9 - - path: results/csv/recalibrated.csv - md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 - - path: results/multiqc - - path: results/preprocessing/mapped/test/test.sorted.cram - # binary changes md5sums on reruns. - - path: results/preprocessing/mapped/test/test.sorted.cram.crai - # binary changes md5sums on reruns. - - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 8de213f4c00fac61a1102633760493df - - 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/fastqc/test-test_L1 - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 48aa760b024d7c0ddd5a66f89a1cb544 - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 71e938314bba70f978271b2b56cb7ad3 - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 0786d56af0672eaef44b29f4ed5c12cb - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: b8719430e56a58f734884bb422a7b8fa - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: e3235323f455414ee3acc7144e659caf - - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: 48aa760b024d7c0ddd5a66f89a1cb544 - - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 71e938314bba70f978271b2b56cb7ad3 - - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: 0786d56af0672eaef44b29f4ed5c12cb - - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: b8719430e56a58f734884bb422a7b8fa - - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: e3235323f455414ee3acc7144e659caf - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 55ddd2d98552a1483bf2a965f19d8da4 - - path: results/reports/samtools/test/test.sorted.cram.stats - md5sum: 59d921ed3970e19145fbae75966de3e3 - - 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 -- name: Run default pipeline with skipping MarkDuplicates with save_mapped & save_output_as_bam - command: nextflow run main.nf -profile test,skip_markduplicates --save_mapped --save_output_as_bam - tags: - - preprocessing - - skip_markduplicates - files: - - path: results/csv/mapped.csv - md5sum: 7f21bf40d3fbc248ee2ea3fdf0f7cdb2 - - path: results/csv/recalibrated.csv - md5sum: 3ddc20eb105fdcc483945afd7d7d238c - - path: results/multiqc - - path: results/preprocessing/mapped/test/test.sorted.bam - # binary changes md5sums on reruns. - - path: results/preprocessing/mapped/test/test.sorted.bam.bai - # binary changes md5sums on reruns. - - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 8de213f4c00fac61a1102633760493df - - path: results/preprocessing/recalibrated/test/test.recal.bam - # binary changes md5sums on reruns. - - path: results/preprocessing/recalibrated/test/test.recal.bam.bai - # binary changes md5sums on reruns. - - path: results/reports/fastqc/test-test_L1 - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 48aa760b024d7c0ddd5a66f89a1cb544 - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 71e938314bba70f978271b2b56cb7ad3 - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 0786d56af0672eaef44b29f4ed5c12cb - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: b8719430e56a58f734884bb422a7b8fa - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: e3235323f455414ee3acc7144e659caf - - path: results/reports/mosdepth/test/test.sorted.mosdepth.global.dist.txt - md5sum: 48aa760b024d7c0ddd5a66f89a1cb544 - - path: results/reports/mosdepth/test/test.sorted.mosdepth.region.dist.txt - md5sum: 71e938314bba70f978271b2b56cb7ad3 - - path: results/reports/mosdepth/test/test.sorted.mosdepth.summary.txt - md5sum: 0786d56af0672eaef44b29f4ed5c12cb - - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz - md5sum: b8719430e56a58f734884bb422a7b8fa - - path: results/reports/mosdepth/test/test.sorted.regions.bed.gz.csi - md5sum: e3235323f455414ee3acc7144e659caf - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 55ddd2d98552a1483bf2a965f19d8da4 - - path: results/reports/samtools/test/test.sorted.cram.stats - md5sum: 59d921ed3970e19145fbae75966de3e3 - - 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 diff --git a/tests/test_skip_qc.yml b/tests/test_skip_qc.yml deleted file mode 100644 index 6cb6ee5eff..0000000000 --- a/tests/test_skip_qc.yml +++ /dev/null @@ -1,65 +0,0 @@ -- name: Run default pipeline with skipping all QC steps - command: nextflow run main.nf -profile test --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools - tags: - - skip_qc - - preprocessing - files: - - path: results/csv/markduplicates.csv - md5sum: 0d6120bb99e92f6810343270711ca53e - - path: results/csv/markduplicates_no_table.csv - md5sum: 2a2d3d4842befd4def39156463859ee3 - - path: results/csv/recalibrated.csv - md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 - - 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: 4ac774bf5f1157e77426fd82f5ac0fbe - - 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/multiqc - should_exist: false - - path: results/reports/fastqc - should_exist: false - - path: results/reports/markduplicates - should_exist: false - - path: results/reports/mosdepth - should_exist: false - - path: results/reports/samtools - should_exist: false - -- name: Run spark pipeline with skipping all QC steps - command: nextflow run main.nf -profile test,use_gatk_spark --skip_tools fastqc,markduplicates_report,mosdepth,multiqc,samtools - tags: - - skip_qc - - preprocessing - files: - - path: results/csv/markduplicates.csv - md5sum: 0d6120bb99e92f6810343270711ca53e - - path: results/csv/markduplicates_no_table.csv - md5sum: 2a2d3d4842befd4def39156463859ee3 - - path: results/csv/recalibrated.csv - md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 - - path: results/preprocessing/markduplicates/test/test.md.cram - md5sum: cf0ebfe288ee7164cd2fcd028bda1887 - - path: results/preprocessing/markduplicates/test/test.md.cram.crai - md5sum: 2136b37eca3e806c77c39ee823231679 - - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 5b6e5078b4a90f6cb982fa0f0df616c2 - - path: results/preprocessing/recalibrated/test/test.recal.cram - md5sum: 1c168110f006bacba2ed8783bb5a3dee - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - md5sum: 1c91543c9f75bc354274b1a1da745ee3 - - path: results/multiqc - should_exist: false - - path: results/reports/fastqc - should_exist: false - - path: results/reports/markduplicates - should_exist: false - - path: results/reports/mosdepth - should_exist: false - - path: results/reports/samtools - should_exist: false diff --git a/tests/test_split_fastq.yml b/tests/test_split_fastq.yml deleted file mode 100644 index 49b17b39d4..0000000000 --- a/tests/test_split_fastq.yml +++ /dev/null @@ -1,57 +0,0 @@ -- name: Run split fastq module - command: nextflow run main.nf -profile test,split_fastq - tags: - - split_fastq - files: - - path: results/csv/markduplicates.csv - md5sum: 0d6120bb99e92f6810343270711ca53e - - path: results/csv/markduplicates_no_table.csv - md5sum: 2a2d3d4842befd4def39156463859ee3 - - path: results/csv/recalibrated.csv - md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 - - path: results/preprocessing/fastp/test/0001.test-test_L1_1.fastp.fastq.gz - md5sum: dc56d2161f02a4a9f79fe2c4a646aadc - - path: results/preprocessing/fastp/test/0001.test-test_L1_2.fastp.fastq.gz - md5sum: 3ed01c8e26fcc25859322e4f9a07a217 - - path: results/preprocessing/fastp/test/0002.test-test_L1_1.fastp.fastq.gz - md5sum: 16c3b700adf22dbac28ffb6b63a9615b - - path: results/preprocessing/fastp/test/0002.test-test_L1_2.fastp.fastq.gz - md5sum: 7efff2539c8cb03e0cc5eaab442870e5 - - 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: 36b9cec9f69726d3acb0b42685100eb2 - - 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/fastp/test - - path: results/reports/fastqc/test-test_L1 - - path: results/reports/markduplicates/test/test.md.cram.metrics - contains: ["test 8741 445 85 523841 3811 0 0 0.395701", "1.0 445 445"] - - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 3fae37c0bcc0742b89a5b5d01978f593 - - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 2d5a9d4f8a19ec0aa962ee5912a506c2 - - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 970e3faef6be251e32b3af06ed7f5cfc - - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 1903e2eedef8d11176fb30d0bb934b13 - - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: 1b65ac38cd96783394e0cf9b7bdd5bc2 - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 3fae37c0bcc0742b89a5b5d01978f593 - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 2d5a9d4f8a19ec0aa962ee5912a506c2 - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 970e3faef6be251e32b3af06ed7f5cfc - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 1903e2eedef8d11176fb30d0bb934b13 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: 1b65ac38cd96783394e0cf9b7bdd5bc2 - - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 44c873922c844b85c0920d22c98b08cf - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 5ad46c4c701943dfc67604ed34c1c69e diff --git a/tests/test_strelka.yml b/tests/test_strelka.yml new file mode 100644 index 0000000000..d6c0f4551a --- /dev/null +++ b/tests/test_strelka.yml @@ -0,0 +1,315 @@ +- name: Skip variant calling on matched normal + command: nextflow run main.nf -profile test,variantcalling_channels --tools strelka --only_paired_variant_calling + 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 +- name: Run variant calling on germline sample with strelka + command: nextflow run main.nf -profile test,tools_germline --tools strelka + 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 +- name: Run variant calling on germline sample with strelka without intervals + command: nextflow run main.nf -profile test,tools_germline --tools strelka --no_intervals + 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 +- name: Run variant calling on tumor only sample with strelka + command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka + tags: + - strelka + - tumor_only + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: 8d2a5e0ad12781c99e773b828e478d35 + - path: results/multiqc + - path: results/reports/bcftools/strelka/sample2/sample2.strelka.variants.bcftools_stats.txt + # 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", "72 458 47880 0.00956558 6 20 0.3", "314 463 47899 0.00966617 1 1 1"] + - 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/strelka + should_exist: false +- name: Run variant calling on tumor only sample with strelka without intervals + command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka --no_intervals + tags: + - no_intervals + - strelka + - tumor_only + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: 8d2a5e0ad12781c99e773b828e478d35 + - 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/sample2/sample2.strelka.variants.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.FILTER.summary + md5sum: d1dcce19d82ced016724ace746e95d01 + - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.TsTv.count + md5sum: 9de35bbe9ebe45166b6bd195717f733a + - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.TsTv.qual + # conda changes md5sums for test. + - 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/strelka + should_exist: false +- name: Run variant calling on somatic sample with strelka + command: nextflow run main.nf -profile test,tools_somatic --tools strelka + 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 +- name: Run variant calling on somatic sample with strelka without intervals + command: nextflow run main.nf -profile test,tools_somatic --tools strelka --no_intervals + 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 diff --git a/tests/test_strelka_bp.yml b/tests/test_strelka_bp.yml new file mode 100644 index 0000000000..d81907b5eb --- /dev/null +++ b/tests/test_strelka_bp.yml @@ -0,0 +1,187 @@ +- name: Run variant calling on somatic sample with Strelka BP + command: nextflow run main.nf -profile test,tools_somatic --tools strelka,manta + 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: e7ca7e9fe76ce12198fd54ec9a64fad4 + - 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: e7ca7e9fe76ce12198fd54ec9a64fad4 + - 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: e7ca7e9fe76ce12198fd54ec9a64fad4 + - 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 +- 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 + 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 diff --git a/tests/test_targeted.yml b/tests/test_targeted.yml deleted file mode 100644 index e2d19b765b..0000000000 --- a/tests/test_targeted.yml +++ /dev/null @@ -1,58 +0,0 @@ -- name: Run default pipeline with target bed - command: nextflow run main.nf -profile test,targeted - tags: - - preprocessing - - targeted - files: - - path: results/csv/markduplicates.csv - md5sum: 0d6120bb99e92f6810343270711ca53e - - path: results/csv/markduplicates_no_table.csv - md5sum: 2a2d3d4842befd4def39156463859ee3 - - path: results/csv/recalibrated.csv - md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 - - 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: c990e4f1b7dbd5a3a623882a54ae2bf2 - - 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/fastqc/test-test_L1 - - path: results/reports/markduplicates/test/test.md.cram.metrics - contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] - - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 5a0679057c530e5945c9c5a3a17312dc - - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 - - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: dcc9ab2bf3248903e02d8da87e678977 - - path: results/reports/mosdepth/test/test.md.per-base.bed.gz - md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 - - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi - md5sum: b0ab630c3241fbd7581b7a38d944ff8b - - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 91e0d531f1bab64711ecefe52bfc8255 - - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 0b3162def977123809598639f7698121 - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: a8455eb2947de529abfa62b303986e0f - - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: d9fa560ff78ae106cfee9db2c90801b5 - - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 4816eeb9af254ca40177b08cf11b98d2 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 91e0d531f1bab64711ecefe52bfc8255 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 52411f93d9b5382342b40a351c2e313c - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 5ed26e702d5c2238a1f3cdc5e5b44f98 diff --git a/tests/test_tiddit.yml b/tests/test_tiddit.yml new file mode 100644 index 0000000000..2c7a51d0d3 --- /dev/null +++ b/tests/test_tiddit.yml @@ -0,0 +1,98 @@ +- name: Run variant calling on somatic sample with tiddit + command: nextflow run main.nf -profile test,tools_somatic --tools tiddit + tags: + - tiddit + - somatic + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: 76b499e35c128d67b0606ea561bf70e0 + - path: results/multiqc + - path: results/reports/bcftools/tiddit/sample3/sample3.tiddit.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/bcftools/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/vcftools/tiddit/sample3/sample3.tiddit.FILTER.summary + md5sum: 1ce42d34e4ae919afb519efc99146423 + - path: results/reports/vcftools/tiddit/sample3/sample3.tiddit.TsTv.count + md5sum: fa27f678965b7cba6a92efcd039f802a + - path: results/reports/vcftools/tiddit/sample3/sample3.tiddit.TsTv.qual + md5sum: bc68ae4e688e9fb772b457069e604883 + - path: results/reports/vcftools/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.FILTER.summary + md5sum: 1ce42d34e4ae919afb519efc99146423 + - path: results/reports/vcftools/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.TsTv.count + md5sum: 8dcfdbcaac118df1d5ad407dd2af699f + - path: results/reports/vcftools/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.TsTv.qual + md5sum: bc68ae4e688e9fb772b457069e604883 + - path: results/variant_calling/tiddit/sample3/sample3.tiddit.ploidies.tab + md5sum: d65f8aa5bb136f77c23264640481f047 + - path: results/variant_calling/tiddit/sample3/sample3.tiddit.vcf.gz + # conda changes md5sums for test. + - path: results/variant_calling/tiddit/sample3/sample3.tiddit.vcf.gz.tbi + # conda changes md5sums for test. + - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.normal.vcf.gz + # conda changes md5sums for test. + - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.normal.vcf.gz.tbi + # conda changes md5sums for test. + - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.ploidies.tab + # conda changes md5sums for test. + - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.tumor.vcf.gz + # conda changes md5sums for test. + - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.tumor.vcf.gz.tbi + # conda changes md5sums for test. + - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.vcf.gz + # conda changes md5sums for test. + - path: results/tiddit + should_exist: false +- name: Run variant calling on germline sample with tiddit + command: nextflow run main.nf -profile test,tools_germline --tools tiddit + tags: + - tiddit + - germline + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: cd458ebee25e1fb1258d2f390e54c736 + - path: results/multiqc + - path: results/reports/bcftools/tiddit/sample1/sample1.tiddit.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/vcftools/tiddit/sample1/sample1.tiddit.FILTER.summary + md5sum: 1ce42d34e4ae919afb519efc99146423 + - path: results/reports/vcftools/tiddit/sample1/sample1.tiddit.TsTv.count + md5sum: fa27f678965b7cba6a92efcd039f802a + - path: results/reports/vcftools/tiddit/sample1/sample1.tiddit.TsTv.qual + md5sum: bc68ae4e688e9fb772b457069e604883 + - path: results/variant_calling/tiddit/sample1/sample1.tiddit.ploidies.tab + md5sum: d65f8aa5bb136f77c23264640481f047 + - path: results/variant_calling/tiddit/sample1/sample1.tiddit.vcf.gz + # conda changes md5sums for test. + - path: results/variant_calling/tiddit/sample1/sample1.tiddit.vcf.gz.tbi + # conda changes md5sums for test. + - path: results/tiddit + should_exist: false +- name: Run variant calling on tumor_only sample with tiddit + command: nextflow run main.nf -profile test,tools_tumoronly --tools tiddit + tags: + - tiddit + - tumor_only + - variant_calling + files: + - path: results/csv/variantcalled.csv + md5sum: 15076bb78912fe51006e83934c376fc2 + - path: results/multiqc + - path: results/reports/bcftools/tiddit/sample2/sample2.tiddit.bcftools_stats.txt + # conda changes md5sums for test. + - path: results/reports/vcftools/tiddit/sample2/sample2.tiddit.FILTER.summary + md5sum: 1ce42d34e4ae919afb519efc99146423 + - path: results/reports/vcftools/tiddit/sample2/sample2.tiddit.TsTv.count + md5sum: fa27f678965b7cba6a92efcd039f802a + - path: results/reports/vcftools/tiddit/sample2/sample2.tiddit.TsTv.qual + md5sum: bc68ae4e688e9fb772b457069e604883 + - path: results/variant_calling/tiddit/sample2/sample2.tiddit.ploidies.tab + md5sum: 0f01874e20df10ecc7418d4537c7aa82 + - path: results/variant_calling/tiddit/sample2/sample2.tiddit.vcf.gz + # conda changes md5sums for test. + - path: results/variant_calling/tiddit/sample2/sample2.tiddit.vcf.gz.tbi + # conda changes md5sums for test. + - path: results/tiddit + should_exist: false diff --git a/tests/test_tools.yml b/tests/test_tools.yml deleted file mode 100644 index fa81e2c270..0000000000 --- a/tests/test_tools.yml +++ /dev/null @@ -1,1750 +0,0 @@ -- name: Run variant calling on somatic samples with cnvkit - command: nextflow run main.nf -profile test,tools_somatic --tools cnvkit - tags: - - cnvkit - - somatic - - variant_calling - - copy_number_calling - files: - - path: results/multiqc - - path: results/variant_calling/cnvkit/sample3/multi_intervals.antitarget.bed - md5sum: 3d4d20f9f23b39970865d29ef239d20b - - path: results/variant_calling/cnvkit/sample3/multi_intervals.target.bed - md5sum: 86d30493bb2e619a93f4ebc2923d29f3 - - path: results/variant_calling/cnvkit/sample3/reference.cnn - md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec - - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted-diagram.pdf - # binary changes md5sums on reruns. - - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted-scatter.png - md5sum: c96b97b9ce948daf3437ccecfd67a4a7 - - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn - md5sum: fe1248aa91fad7769303bb4c031d55ca - - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.bintest.cns - md5sum: e55667a75d7d8eaec2efd3b611f15379 - - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.call.cns - md5sum: 9968e02ef2f11ed22e2789c053f7159c - - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.cnr - md5sum: 3f0fe46574d0f7137f779e7ac1c2362d - - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.cns - md5sum: 0b2b81d391965488b8634a2b802b69cd - - path: results/variant_calling/cnvkit/sample3/test.paired_end.recalibrated.sorted.targetcoverage.cnn - md5sum: 79aae7e9c135fb8c65f8fbda12610faf - - path: results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.antitarget.bed - md5sum: 3d4d20f9f23b39970865d29ef239d20b - - path: results/variant_calling/cnvkit/sample4_vs_sample3/multi_intervals.target.bed - md5sum: 86d30493bb2e619a93f4ebc2923d29f3 - - path: results/variant_calling/cnvkit/sample4_vs_sample3/reference.cnn - md5sum: 59ec306bb820684b1f6f277d67cb2d92 - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn - md5sum: fe1248aa91fad7769303bb4c031d55ca - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test.paired_end.recalibrated.sorted.targetcoverage.cnn - md5sum: 79aae7e9c135fb8c65f8fbda12610faf - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted-diagram.pdf - # binary changes md5sums on reruns. - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted-scatter.png - md5sum: acd87dfb61db5910afaea34053aed561 - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn - md5sum: 067115082c4af4b64d58c0dc3a3642e4 - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.bintest.cns - md5sum: e9a260b81a34d8bc75330435d2a5e8da - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.call.cns - md5sum: c7d7fd87b27e103f73988ae307450e82 - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cnr - md5sum: 26c506866198d46610c71fa6c0f9e381 - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.cns - md5sum: 83510b274c24a2671a962477a1ceb436 - - path: results/variant_calling/cnvkit/sample4_vs_sample3/test2.paired_end.recalibrated.sorted.targetcoverage.cnn - md5sum: b4a49faf170e436ec32dcc21ccc3ce8f - - path: results/cnvkit - should_exist: false -- name: Run variant calling on tumor_only sample with cnvkit - command: nextflow run main.nf -profile test,tools_tumoronly --tools cnvkit - tags: - - cnvkit - - tumor_only - - variant_calling - - copy_number_calling - files: - - path: results/multiqc - - path: results/variant_calling/cnvkit/sample2/cnvkit.reference.antitarget-tmp.bed - md5sum: 3d4d20f9f23b39970865d29ef239d20b - - path: results/variant_calling/cnvkit/sample2/cnvkit.reference.target-tmp.bed - md5sum: 657b25dbda8516624efa8cb2cf3716ca - - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted-diagram.pdf - # binary changes md5sums on reruns. - - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted-scatter.png - md5sum: 7f2d2380309d5e19c8942131890d0e39 - - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.antitargetcoverage.cnn - md5sum: 067115082c4af4b64d58c0dc3a3642e4 - - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.bintest.cns - md5sum: f6adc75a0a86b7a921eca1b79a394cb0 - - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.call.cns - md5sum: f7caeca04aba28b125ce26b511f42afb - - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.cnr - md5sum: d9bdb71ce807051369577ee7f807a40c - - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.cns - md5sum: 2b56aac606ba6183d018b30ca58afcec - - path: results/variant_calling/cnvkit/sample2/test2.paired_end.recalibrated.sorted.targetcoverage.cnn - md5sum: e6d0190c1c37ce6e41f76ca5b24ccca3 - - path: results/cnvkit - should_exist: false -- name: Run variant calling on germline sample with cnvkit - command: nextflow run main.nf -profile test,tools_germline --tools cnvkit - tags: - - cnvkit - - germline - - variant_calling - - copy_number_calling - files: - - path: results/multiqc - - path: results/variant_calling/cnvkit/sample1/multi_intervals.antitarget.bed - md5sum: 3d4d20f9f23b39970865d29ef239d20b - - path: results/variant_calling/cnvkit/sample1/multi_intervals.target.bed - md5sum: 86d30493bb2e619a93f4ebc2923d29f3 - - path: results/variant_calling/cnvkit/sample1/reference.cnn - md5sum: a09ee4be5dda1cf0f68073bdb3aad8ec - - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted-diagram.pdf - # binary changes md5sums on reruns. - - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted-scatter.png - md5sum: c96b97b9ce948daf3437ccecfd67a4a7 - - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.antitargetcoverage.cnn - md5sum: fe1248aa91fad7769303bb4c031d55ca - - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.bintest.cns - md5sum: e55667a75d7d8eaec2efd3b611f15379 - - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.call.cns - md5sum: 9968e02ef2f11ed22e2789c053f7159c - - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.cnr - md5sum: 3f0fe46574d0f7137f779e7ac1c2362d - - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.cns - md5sum: 0b2b81d391965488b8634a2b802b69cd - - path: results/variant_calling/cnvkit/sample1/test.paired_end.recalibrated.sorted.targetcoverage.cnn - md5sum: 79aae7e9c135fb8c65f8fbda12610faf - - path: results/cnvkit - should_exist: false -- name: Run variant calling on somatic samples with controlfreec - command: nextflow run main.nf -profile test,tools_somatic --tools controlfreec - tags: - - controlfreec - - somatic - - variant_calling - - copy_number_calling - files: - - path: results/multiqc - - path: results/untar/chromosomes/chr21.fasta - md5sum: 69bd44ef67566a76d6cbb8aa4a25ae35 - - path: results/variant_calling/controlfreec/sample4_vs_sample3/config.txt - contains: - [ - "BedGraphOutput = TRUE", - "minExpectedGC = 0", - "maxThreads = 2", - "noisyData = TRUE", - "readCountThreshold = 1", - "sex = XX", - "window = 10", - ] - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.bed - md5sum: 833920178e4f40a296d8eab029caf086 - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.circos.txt - md5sum: 92ce5ce97b27a7214dfa9c2cb20cf854 - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz_control.cpn - md5sum: 508a003da85b186d9a60d867ef7cdf15 - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.p.value.txt - # binary changes md5sums on reruns. - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_BAF.txt - # binary changes md5sums on reruns. - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_CNVs - # binary changes md5sums on reruns. - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_info.txt - md5sum: 271271719c576d9218bdc859850e54ee - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_ratio.BedGraph - md5sum: 5d3321af93678f16878d59e01d3a87d3 - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_ratio.txt - # binary changes md5sums on reruns. - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_sample.cpn - md5sum: befe1706c61464635a76c7323a6bd2a2 - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.png - # binary changes md5sums on reruns. - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.log2.png - # binary changes md5sums on reruns. - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.png - # binary changes md5sums on reruns. - - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz - # binary changes md5sums on reruns. - - path: results/cnvkit - should_exist: false -- name: Run variant calling on somatic samples with controlfreec without intervals - command: nextflow run main.nf -profile test,tools_somatic --tools controlfreec --no_intervals -stub-run - tags: - - controlfreec - - no_intervals - - somatic - - variant_calling - - copy_number_calling - files: - - 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/untar/chromosomes - - path: results/variant_calling/controlfreec/sample4_vs_sample3/GC_profile.sample4_vs_sample3.cpn - md5sum: d41d8cd98f00b204e9800998ecf8427e # This is the md5sum of an empty file. Are all these files suppose to be empty? - - path: results/variant_calling/controlfreec/sample4_vs_sample3/config.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.bed - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.circos.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.p.value.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.png - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_CNVs - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_info.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.BedGraph - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.log2.png - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.png - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_sample.cpn - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz - # binary changes md5sums on reruns. - - path: results/controlfreec - should_exist: false - - path: results/mpileup - should_exist: false -- name: Run variant calling on tumor_only sample with controlfreec - command: nextflow run main.nf -profile test,tools_tumoronly --tools controlfreec -stub-run - tags: - - controlfreec - - tumor_only - - variant_calling - - copy_number_calling - files: - - path: results/multiqc - - path: results/variant_calling/controlfreec/sample2/GC_profile.sample2.cpn - md5sum: d41d8cd98f00b204e9800998ecf8427e # This is the md5sum of an empty file. Are all these files suppose to be empty? - - path: results/variant_calling/controlfreec/sample2/config.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample2/sample2.bed - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample2/sample2.circos.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample2/sample2.p.value.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample2/sample2_BAF.png - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample2/sample2_BAF.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample2/sample2_CNVs - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample2/sample2_info.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample2/sample2_ratio.BedGraph - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample2/sample2_ratio.log2.png - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample2/sample2_ratio.png - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample2/sample2_ratio.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/controlfreec/sample2/sample2_sample.cpn - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: results/variant_calling/mpileup/sample2/sample2.tumor.mpileup.gz - # binary changes md5sums on reruns. - - path: results/controlfreec - should_exist: false - - path: results/mpileup - should_exist: false -- name: Run variant calling on germline sample with deepvariant - command: nextflow run main.nf -profile test,tools_germline --tools deepvariant - tags: - - deepvariant - - germline - - variant_calling - files: - - path: results/multiqc - - path: results/reports/bcftools/deepvariant/sample1/sample1.deepvariant.bcftools_stats.txt - md5sum: 433aa535e9ce72acddca7be36b12238b - - path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.FILTER.summary - md5sum: f97d30123c7e20c704e9a8a73170661e - - path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.TsTv.count - md5sum: 1f546d259ddc493736507b35ee520dc4 - - path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.TsTv.qual - md5sum: 437d6a802b10f05fa1601166eb6b7d48 - - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/deepvariant - should_exist: false -- name: Run variant calling on germline sample with deepvariant without intervals - command: nextflow run main.nf -profile test,tools_germline --tools deepvariant --no_intervals - tags: - - deepvariant - - germline - - no_intervals - - variant_calling - files: - - 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/deepvariant/sample1/sample1.deepvariant.bcftools_stats.txt - md5sum: 0d8602284347cb5acf1c264a301f5093 - - path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.FILTER.summary - md5sum: cffb486232d067db80616c3129bf1322 - - path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.TsTv.count - md5sum: bbd541f33c490df06fee5feb2f6e2c7f - - path: results/reports/vcftools/deepvariant/sample1/sample1.deepvariant.TsTv.qual - md5sum: 037063e030edec5fb4e784b1f6c8954f - - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.g.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/deepvariant/sample1/sample1.deepvariant.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/deepvariant - should_exist: false -- name: Run variant calling on germline sample with freebayes - command: nextflow run main.nf -profile test,targeted --tools freebayes - tags: - - freebayes - - germline - - variant_calling - files: - - path: results/csv/markduplicates.csv - md5sum: 0d6120bb99e92f6810343270711ca53e - - path: results/csv/markduplicates_no_table.csv - md5sum: 2a2d3d4842befd4def39156463859ee3 - - path: results/csv/recalibrated.csv - md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 - - path: results/csv/variantcalled.csv - md5sum: 0cc6a67fedb2ef9ce97e463d310f9f30 - - 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: c990e4f1b7dbd5a3a623882a54ae2bf2 - - 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/bcftools/freebayes/test/test.freebayes.bcftools_stats.txt - md5sum: 16c7673085520b66bd47f59fbf8a7e0e - - path: results/reports/fastqc/test-test_L1 - - path: results/reports/markduplicates/test/test.md.cram.metrics - contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] - - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 5a0679057c530e5945c9c5a3a17312dc - - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 - - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: dcc9ab2bf3248903e02d8da87e678977 - - path: results/reports/mosdepth/test/test.md.per-base.bed.gz - md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 - - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi - md5sum: b0ab630c3241fbd7581b7a38d944ff8b - - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 91e0d531f1bab64711ecefe52bfc8255 - - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 0b3162def977123809598639f7698121 - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: a8455eb2947de529abfa62b303986e0f - - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: d9fa560ff78ae106cfee9db2c90801b5 - - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 4816eeb9af254ca40177b08cf11b98d2 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 91e0d531f1bab64711ecefe52bfc8255 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 52411f93d9b5382342b40a351c2e313c - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 5ed26e702d5c2238a1f3cdc5e5b44f98 - - path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary - md5sum: 43d53e36cbb1091f915b2499e545b41e - - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count - md5sum: 650f3dc78c5aaaecfe8ffa3d499e812f - - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.qual - contains: ["0 0 0 -nan 82 29 2.82759", "1.1 196 35 5.6 57 24 2.375", "3.16 205 38 5.39474 49 20 2.45"] - - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/freebayes - should_exist: false -- name: Run variant calling on germline sample with freebayes without intervals - command: nextflow run main.nf -profile test --tools freebayes --no_intervals - tags: - - freebayes - - germline - - no_intervals - - variant_calling - files: - - path: results/csv/markduplicates.csv - md5sum: 0d6120bb99e92f6810343270711ca53e - - path: results/csv/markduplicates_no_table.csv - md5sum: 2a2d3d4842befd4def39156463859ee3 - - path: results/csv/recalibrated.csv - md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 - - path: results/csv/variantcalled.csv - md5sum: 0cc6a67fedb2ef9ce97e463d310f9f30 - - 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/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: 4ac774bf5f1157e77426fd82f5ac0fbe - - 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/bcftools/freebayes/test/test.freebayes.bcftools_stats.txt - md5sum: f66375a00d692d67df46c129147008b2 - - path: results/reports/fastqc/test-test_L1 - - path: results/reports/markduplicates/test/test.md.cram.metrics - contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] - - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 76fa71922a3f748e507c2364c531dfcb - - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: abc5df85e302b79985627888870882da - - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: d536456436eb275159b8c6af83213d80 - - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 38fe39894abe62e38f8ac214cba64f2b - - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: b1c2a861f64e20a94108a6de3b76c582 - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 76fa71922a3f748e507c2364c531dfcb - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: abc5df85e302b79985627888870882da - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: d536456436eb275159b8c6af83213d80 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 38fe39894abe62e38f8ac214cba64f2b - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: b1c2a861f64e20a94108a6de3b76c582 - - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 52411f93d9b5382342b40a351c2e313c - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: d80ad11b8e308a3d5b1fb6f8e13cef38 - - path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary - md5sum: 76c5919541536c12b5c8a6094d6d78d5 - - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count - md5sum: 0a0464beef110bc0f3c5a35d022b528e - - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.qual - contains: ["0 0 0 -nan 325 86 3.77907", "27.5873 359 84 4.27381 39 13 3", "40.5188 368 87 4.22989 30 10 3"] - - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/freebayes - should_exist: false -- name: Run variant calling on somatic sample with freebayes - command: nextflow run main.nf -profile test,pair,targeted --tools freebayes - tags: - - freebayes - - somatic - - variant_calling - files: - - path: results/csv/markduplicates.csv - md5sum: e8e587ac25253ff7ab8f1cc66d410c98 - - path: results/csv/markduplicates_no_table.csv - md5sum: 617574c9b607e5daaf4ad56d48982247 - - path: results/csv/recalibrated.csv - md5sum: 008dff17e2a0d96ef9c1cae12fcab6ab - - path: results/csv/variantcalled.csv - md5sum: b31f56256a1cfa839a2ea7f7ba6c1c45 - - 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/markduplicates/test2/test2.md.cram - # binary changes md5sums on reruns. - - path: results/preprocessing/markduplicates/test2/test2.md.cram.crai - # binary changes md5sums on reruns. - - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: c990e4f1b7dbd5a3a623882a54ae2bf2 - - path: results/preprocessing/recal_table/test2/test2.recal.table - md5sum: 00d6877d68d622d81e4d633c4e340e7e - - 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/preprocessing/recalibrated/test2/test2.recal.cram - # binary changes md5sums on reruns. - - path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai - # binary changes md5sums on reruns. - - path: results/reports/bcftools/freebayes/test/test.freebayes.bcftools_stats.txt - md5sum: 16c7673085520b66bd47f59fbf8a7e0e - - path: results/reports/bcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.bcftools_stats.txt - md5sum: 001709e5eeca385908e31ba370f53381 - - path: results/reports/fastqc/test-test_L1 - - path: results/reports/markduplicates/test/test.md.cram.metrics - contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] - - path: results/reports/markduplicates/test2/test2.md.cram.metrics - contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"] - - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 5a0679057c530e5945c9c5a3a17312dc - - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 - - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: dcc9ab2bf3248903e02d8da87e678977 - - path: results/reports/mosdepth/test/test.md.per-base.bed.gz - md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 - - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi - md5sum: b0ab630c3241fbd7581b7a38d944ff8b - - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 91e0d531f1bab64711ecefe52bfc8255 - - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 0b3162def977123809598639f7698121 - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 835fdc6fa52cc33e6fb76c0c20a8a6c3 - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: a8455eb2947de529abfa62b303986e0f - - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: d9fa560ff78ae106cfee9db2c90801b5 - - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: 4816eeb9af254ca40177b08cf11b98d2 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 91e0d531f1bab64711ecefe52bfc8255 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt - md5sum: f25166c3a0051bb4d8c11a210278de6c - - path: results/reports/mosdepth/test2/test2.md.mosdepth.region.dist.txt - md5sum: 3211135329e4077bd9bf0ba488e14371 - - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt - md5sum: ce0eb6d33c6d0dc720fbc6d1811abef8 - - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz - md5sum: 55c160e8f3c8c7761524646426611f6b - - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz.csi - md5sum: 4205a09ede17cdbdaad45e3553f73105 - - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz - md5sum: 1dd426a45f967a9f37dcddcaea29a582 - - path: results/reports/mosdepth/test2/test2.md.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt - md5sum: a1ef7e662ce993da4668e804952014ce - - path: results/reports/mosdepth/test2/test2.recal.mosdepth.region.dist.txt - md5sum: 3211135329e4077bd9bf0ba488e14371 - - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt - md5sum: 70ad653c0c98baeeaf5085f1209a7bdb - - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz - md5sum: 250a9f15a7d3f102435fa98adccf48a3 - - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz.csi - md5sum: 8072f447199c60f24b01eede8b557333 - - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz - md5sum: 1dd426a45f967a9f37dcddcaea29a582 - - path: results/reports/mosdepth/test2/test2.recal.regions.bed.gz.csi - md5sum: c6d1ac97ef4dfe43731c8368d8391cab - - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 52411f93d9b5382342b40a351c2e313c - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 5ed26e702d5c2238a1f3cdc5e5b44f98 - - path: results/reports/samtools/test2/test2.md.cram.stats - md5sum: 60152dbf1e109d4c407c151204388109 - - path: results/reports/samtools/test2/test2.recal.cram.stats - md5sum: 53a0b34b67fdf90ea68fac8ea744b576 - - path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary - md5sum: 43d53e36cbb1091f915b2499e545b41e - - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count - md5sum: 650f3dc78c5aaaecfe8ffa3d499e812f - - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.qual - contains: ["0 0 0 -nan 82 29 2.82759", "1.1 196 35 5.6 57 24 2.375", "3.16 205 38 5.39474 49 20 2.45"] - - path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.FILTER.summary - md5sum: ac61b178a3e15efb861b34f16d80fb67 - - path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.TsTv.count - md5sum: d7c0e0afd59f87dc4685487c0d497575 - - path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.TsTv.qual - # the text-based file test2_vs_test.freebayes.TsTv.qual seemingly changes content on reruns! - - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/freebayes - should_exist: false - -- name: Run variant calling on somatic sample with freebayes without intervals - command: nextflow run main.nf -profile test,pair,targeted --tools freebayes --no_intervals - tags: - - freebayes - - somatic - - no_intervals - - variant_calling - files: - - path: results/csv/markduplicates.csv - md5sum: e8e587ac25253ff7ab8f1cc66d410c98 - - path: results/csv/markduplicates_no_table.csv - md5sum: 617574c9b607e5daaf4ad56d48982247 - - path: results/csv/recalibrated.csv - md5sum: 008dff17e2a0d96ef9c1cae12fcab6ab - - path: results/csv/variantcalled.csv - md5sum: b31f56256a1cfa839a2ea7f7ba6c1c45 - - 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/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/markduplicates/test2/test2.md.cram - # binary changes md5sums on reruns. - - path: results/preprocessing/markduplicates/test2/test2.md.cram.crai - # binary changes md5sums on reruns. - - path: results/preprocessing/recal_table/test/test.recal.table - md5sum: 4ac774bf5f1157e77426fd82f5ac0fbe - - path: results/preprocessing/recal_table/test2/test2.recal.table - md5sum: 0626cd4337eab79b38b5bc5c95e0c003 - - 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/preprocessing/recalibrated/test2/test2.recal.cram - # binary changes md5sums on reruns. - - path: results/preprocessing/recalibrated/test2/test2.recal.cram.crai - # binary changes md5sums on reruns. - - path: results/reports/bcftools/freebayes/test/test.freebayes.bcftools_stats.txt - md5sum: f66375a00d692d67df46c129147008b2 - - path: results/reports/bcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.bcftools_stats.txt - md5sum: 41d9835772fa1326769c2dd94749cbea - - path: results/reports/fastqc/test-test_L1 - - path: results/reports/markduplicates/test/test.md.cram.metrics - contains: ["test 8547 767 84 523391 3882 0 0 0.385081", "1.0 767 767"] - - path: results/reports/markduplicates/test2/test2.md.cram.metrics - contains: ["test2 10103 880 35 523579 4837 2 0 0.408076 193306", "1.0 1 876 876", "100.0 80.515303 0 0"] - - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 5a0679057c530e5945c9c5a3a17312dc - - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 0010c2396a3173c7cf4983abe2eb6a4c - - path: results/reports/mosdepth/test/test.md.per-base.bed.gz - md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 - - path: results/reports/mosdepth/test/test.md.per-base.bed.gz.csi - md5sum: b0ab630c3241fbd7581b7a38d944ff8b - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 5a0679057c530e5945c9c5a3a17312dc - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 0010c2396a3173c7cf4983abe2eb6a4c - - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz - md5sum: 5724f1c6b6a0e63e25ec8a0f38edfda6 - - path: results/reports/mosdepth/test/test.recal.per-base.bed.gz.csi - md5sum: b0ab630c3241fbd7581b7a38d944ff8b - - path: results/reports/mosdepth/test2/test2.md.mosdepth.global.dist.txt - md5sum: f25166c3a0051bb4d8c11a210278de6c - - path: results/reports/mosdepth/test2/test2.md.mosdepth.summary.txt - md5sum: d5e4084de2ea2a0a7b60b2d71c804d4b - - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz - md5sum: 55c160e8f3c8c7761524646426611f6b - - path: results/reports/mosdepth/test2/test2.md.per-base.bed.gz.csi - md5sum: 4205a09ede17cdbdaad45e3553f73105 - - path: results/reports/mosdepth/test2/test2.recal.mosdepth.global.dist.txt - md5sum: f25166c3a0051bb4d8c11a210278de6c - - path: results/reports/mosdepth/test2/test2.recal.mosdepth.summary.txt - md5sum: d5e4084de2ea2a0a7b60b2d71c804d4b - - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz - md5sum: 55c160e8f3c8c7761524646426611f6b - - path: results/reports/mosdepth/test2/test2.recal.per-base.bed.gz.csi - md5sum: 4205a09ede17cdbdaad45e3553f73105 - - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 52411f93d9b5382342b40a351c2e313c - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: d80ad11b8e308a3d5b1fb6f8e13cef38 - - path: results/reports/samtools/test2/test2.md.cram.stats - md5sum: 60152dbf1e109d4c407c151204388109 - - path: results/reports/samtools/test2/test2.recal.cram.stats - md5sum: 029b903797dc228e56d6ab74e677fa21 - - path: results/reports/vcftools/freebayes/test/test.freebayes.FILTER.summary - md5sum: 76c5919541536c12b5c8a6094d6d78d5 - - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.count - md5sum: 0a0464beef110bc0f3c5a35d022b528e - - path: results/reports/vcftools/freebayes/test/test.freebayes.TsTv.qual - contains: ["0 0 0 -nan 325 86 3.77907", "68.8262 377 88 4.28409 20 10 2", "321.335 393 96 4.09375 4 2 2"] - - path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.FILTER.summary - md5sum: 59e9d340b588537655020147e6d93e29 - - path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.TsTv.count - md5sum: 61ad00bb8cd47592b0671fabe26cf8cd - - path: results/reports/vcftools/freebayes/test2_vs_test/test2_vs_test.freebayes.TsTv.qual - # the text-based file test2_vs_test.freebayes.TsTv.qual seemingly changes content on reruns! - - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/freebayes/test/test.freebayes.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/freebayes/test2_vs_test/test2_vs_test.freebayes.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/freebayes - should_exist: false - -# - name: Run variant calling on tumor_only sample with freebayes -# command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes -# tags: -# - freebayes -# - tumor_only -# - variant_calling -# files: -# - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz -# - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz.tbi - -# - name: Run variant calling on tumor_only sample with freebayes without intervals -# command: nextflow run main.nf -profile test,tools_tumoronly --tools freebayes --no_intervals -# tags: -# - freebayes -# - no_intervals -# - tumor_only -# - variant_calling -# files: -# - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz -# - path: results/variant_calling/freebayes/sample2/sample2.freebayes.vcf.gz.tbi - -- name: Run variant calling on germline sample with haplotypecaller - command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling - tags: - - germline - - haplotypecaller - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: d7d86e82902a4f57876b2414a4f812a4 - - 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 - should_exist: false - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - should_exist: false - - path: results/reports/bcftools/haplotypecaller/test/test.haplotypecaller.filtered.bcftools_stats.txt - md5sum: f9cc3809106a42601eafd3b09900750a - - path: results/reports/vcftools/haplotypecaller/test/test.haplotypecaller.filtered.FILTER.summary - md5sum: 4e2ceea7f3ff998004691fd71192d9ee - - path: results/reports/vcftools/haplotypecaller/test/test.haplotypecaller.filtered.TsTv.count - md5sum: b77c120ee5cc0423267200c67d60c663 - - path: results/reports/vcftools/haplotypecaller/test/test.haplotypecaller.filtered.TsTv.qual - md5sum: 1e34357e5848c318f8c2c7d3b041d229 - - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/haplotypecaller - should_exist: false -- name: Run variant calling on germline sample with haplotypecaller without intervals - command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_single_bam.csv --tools haplotypecaller --step variant_calling --no_intervals - tags: - - germline - - haplotypecaller - - no_intervals - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: d7d86e82902a4f57876b2414a4f812a4 - - 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/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 - should_exist: false - - path: results/preprocessing/recalibrated/test/test.recal.cram.crai - should_exist: false - - path: results/reports/bcftools/haplotypecaller/test/test.haplotypecaller.filtered.bcftools_stats.txt - md5sum: f9cc3809106a42601eafd3b09900750a - - path: results/reports/vcftools/haplotypecaller/test/test.haplotypecaller.filtered.FILTER.summary - md5sum: 4e2ceea7f3ff998004691fd71192d9ee - - path: results/reports/vcftools/haplotypecaller/test/test.haplotypecaller.filtered.TsTv.count - md5sum: b77c120ee5cc0423267200c67d60c663 - - path: results/reports/vcftools/haplotypecaller/test/test.haplotypecaller.filtered.TsTv.qual - md5sum: 1e34357e5848c318f8c2c7d3b041d229 - - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.filtered.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/haplotypecaller/test/test.haplotypecaller.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/haplotypecaller - should_exist: false -- name: Run joint germline variant calling with haplotypecaller - command: nextflow run main.nf -profile test,targeted --input ./tests/csv/3.0/mapped_joint_bam.csv --tools haplotypecaller --joint_germline true --step variant_calling - tags: - - germline - - haplotypecaller - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: d2dffdbd2b4f1f26a06637592d24dab3 - - path: results/multiqc - - 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/bcftools/haplotypecaller/joint_variant_calling/joint_germline.bcftools_stats.txt - md5sum: f91f185319e00108870911e0ce1a7ed6 - - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.FILTER.summary - md5sum: 2a4eb7abfb2e64e45d53fdda17530b7f - - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.count - md5sum: 949fa16c755189c23a37f0ea8ecd1b26 - - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.qual - md5sum: 3b3a249fbc26c80ce0acbe91147291ea - - path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/haplotypecaller - should_exist: false -- name: Run variant calling on germline sample with manta - command: nextflow run main.nf -profile test,tools_germline --tools manta - tags: - - germline - - manta - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: 981280af86f69190fdf0639030a80249 - - path: results/multiqc - - path: results/reports/bcftools/manta/sample1/sample1.manta.diploid_sv.bcftools_stats.txt - md5sum: 2afce09f0b53a47acde7f8767fd6fcef - - path: results/reports/vcftools/manta/sample1/sample1.manta.diploid_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample1/sample1.manta.diploid_sv.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/manta/sample1/sample1.manta.diploid_sv.TsTv.qual - md5sum: bc68ae4e688e9fb772b457069e604883 - - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/manta - should_exist: false -- name: Run variant calling on germline sample with manta without intervals - command: nextflow run main.nf -profile test,tools_germline --tools manta --no_intervals - tags: - - germline - - manta - - no_intervals - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: 981280af86f69190fdf0639030a80249 - - 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/sample1/sample1.manta.diploid_sv.bcftools_stats.txt - md5sum: 2afce09f0b53a47acde7f8767fd6fcef - - path: results/reports/vcftools/manta/sample1/sample1.manta.diploid_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample1/sample1.manta.diploid_sv.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/manta/sample1/sample1.manta.diploid_sv.TsTv.qual - md5sum: bc68ae4e688e9fb772b457069e604883 - - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/manta/sample1/sample1.manta.diploid_sv.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/manta - should_exist: false -- name: Run variant calling on tumor_only sample with manta - command: nextflow run main.nf -profile test,tools_tumoronly --tools manta - tags: - - manta - - tumor_only - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: f1051fe647abf202e6332f9a1789c05d - - path: results/multiqc - - path: results/reports/bcftools/manta/sample2/sample2.manta.tumor_sv.bcftools_stats.txt - md5sum: ea7f369ab8edaccc5bf45347bda15dfa - - path: results/reports/vcftools/manta/sample2/sample2.manta.tumor_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample2/sample2.manta.tumor_sv.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/manta/sample2/sample2.manta.tumor_sv.TsTv.qual - md5sum: bc68ae4e688e9fb772b457069e604883 - - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz.tbi - md5sum: e7ca7e9fe76ce12198fd54ec9a64fad4 - - path: results/manta - should_exist: false -- name: Run variant calling on tumor_only sample with manta without intervals - command: nextflow run main.nf -profile test,tools_tumoronly --tools manta --no_intervals - tags: - - manta - - no_intervals - - tumor_only - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: f1051fe647abf202e6332f9a1789c05d - - 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/sample2/sample2.manta.tumor_sv.bcftools_stats.txt - md5sum: ea7f369ab8edaccc5bf45347bda15dfa - - path: results/reports/vcftools/manta/sample2/sample2.manta.tumor_sv.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/manta/sample2/sample2.manta.tumor_sv.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/manta/sample2/sample2.manta.tumor_sv.TsTv.qual - md5sum: bc68ae4e688e9fb772b457069e604883 - - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/manta/sample2/sample2.manta.tumor_sv.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/manta - should_exist: false -- name: Run variant calling on somatic sample with manta - command: nextflow run main.nf -profile test,tools_somatic --tools manta - tags: - - manta - - somatic - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: 3a8861808601994f89d5c55ce5c95dae - - path: results/multiqc - - path: results/reports/bcftools/manta/sample3/sample3.manta.diploid_sv.bcftools_stats.txt - md5sum: 5a5ce4cf9c5f48801851d40772d3ba4b - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.bcftools_stats.txt - md5sum: baa05f77160e6cd985050790334c91e8 - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.bcftools_stats.txt - md5sum: 56c39772dc25e451d8209f608bb16e37 - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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: e7ca7e9fe76ce12198fd54ec9a64fad4 - - 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: e7ca7e9fe76ce12198fd54ec9a64fad4 - - 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: e7ca7e9fe76ce12198fd54ec9a64fad4 - - path: results/manta - should_exist: false -- name: Run variant calling on somatic sample with manta without intervals - command: nextflow run main.nf -profile test,tools_somatic --tools manta --no_intervals - tags: - - manta - - no_intervals - - somatic - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: 3a8861808601994f89d5c55ce5c95dae - - 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 - md5sum: 5a5ce4cf9c5f48801851d40772d3ba4b - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.bcftools_stats.txt - md5sum: baa05f77160e6cd985050790334c91e8 - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.bcftools_stats.txt - md5sum: 56c39772dc25e451d8209f608bb16e37 - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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/manta - should_exist: false -- name: Run variant calling on tumor_only sample to test mpileup - command: nextflow run main.nf -profile test,tools_tumoronly --tools mpileup - tags: - - tumor_only - - mpileup - files: - - path: results/multiqc - - path: results/variant_calling/mpileup/sample2/sample2.tumor.mpileup.gz - # binary changes md5sums on reruns. - - path: results/mpileup - should_exist: false -- name: Run variant calling on tumor_only sample to test mpileup without intervals - command: nextflow run main.nf -profile test,tools_tumoronly --tools mpileup --no_intervals - tags: - - tumor_only - - mpileup - - no_intervals - files: - - 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/variant_calling/mpileup/sample2/sample2.tumor.mpileup.gz - # binary changes md5sums on reruns. - - path: results/mpileup - should_exist: false -- name: Run variant calling on germline sample to test mpileup - command: nextflow run main.nf -profile test,tools_germline --tools mpileup - tags: - - germline - - mpileup - files: - - path: results/multiqc - - path: results/variant_calling/mpileup/sample1/sample1.normal.mpileup.gz - # binary changes md5sums on reruns. - - path: results/mpileup - should_exist: false -- name: Run variant calling on germline sample to test mpileup without intervals - command: nextflow run main.nf -profile test,tools_germline --tools mpileup --no_intervals - tags: - - germline - - mpileup - - no_intervals - files: - - 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/variant_calling/mpileup/sample1/sample1.normal.mpileup.gz - # binary changes md5sums on reruns. - - path: results/mpileup - should_exist: false -- name: Run variant calling on tumor only sample with mutect2 - command: nextflow run main.nf -profile test,tools_tumoronly --tools mutect2 - tags: - - mutect2 - - tumor_only - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: d57c1beba9005e9790a573bd93398b72 - - path: results/multiqc - - path: results/reports/bcftools/mutect2/sample2/sample2.mutect2.filtered.bcftools_stats.txt - md5sum: b0277a18599f8aa01e4b1b42ff0257b1 - - path: results/reports/vcftools/mutect2/sample2/sample2.mutect2.filtered.FILTER.summary - md5sum: ef9bd9a2f41d8872ba25e5616e4c2a5e - - path: results/reports/vcftools/mutect2/sample2/sample2.mutect2.filtered.TsTv.count - md5sum: fe3ff1f0c2ead72f037552727438e00a - - path: results/reports/vcftools/mutect2/sample2/sample2.mutect2.filtered.TsTv.qual - md5sum: 13cc608c3cdc83a12ec53ef78b5aa888 - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.artifactprior.tar.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.contamination.table - md5sum: 46c708c943b453da89a3da08acfdb2a7 - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz.filteringStats.tsv - md5sum: 9a8439d0bb5875f1e673cf592af85ffb - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.pileupsummaries.table - md5sum: 9afe42339f590937166edcf4746c22ec - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.segmentation.table - md5sum: f4643d9319bde4efbfbe516d6fb13052 - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.stats - md5sum: 3cc40a35727af6c5223fb45678f3f172 - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/mutect2 - should_exist: false -- name: Run variant calling on tumor only sample with mutect2 without intervals - command: nextflow run main.nf -profile test,tools_tumoronly --tools mutect2 --no_intervals - tags: - - mutect2 - - no_intervals - - tumor_only - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: d57c1beba9005e9790a573bd93398b72 - - 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/mutect2/sample2/sample2.mutect2.filtered.bcftools_stats.txt - md5sum: a449e85411b3b295685f05915de6098d - - path: results/reports/vcftools/mutect2/sample2/sample2.mutect2.filtered.FILTER.summary - md5sum: 5a833fd50e6efb26d1df2336eb0caf5e - - path: results/reports/vcftools/mutect2/sample2/sample2.mutect2.filtered.TsTv.count - md5sum: f5295a61da80f12babae74fe4e104aad - - path: results/reports/vcftools/mutect2/sample2/sample2.mutect2.filtered.TsTv.qual - md5sum: 13cc608c3cdc83a12ec53ef78b5aa888 - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.artifactprior.tar.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.contamination.table - md5sum: 46c708c943b453da89a3da08acfdb2a7 - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz.filteringStats.tsv - md5sum: e4eac0c602dd25aa61a6dc26a2b61844 - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.filtered.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.pileupsummaries.table - md5sum: fe35b6bc041f2df8bd1f23420af3ddf9 - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.segmentation.table - md5sum: f4643d9319bde4efbfbe516d6fb13052 - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz - # binary changes md5sums on reruns. - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.stats - md5sum: 55ed641e16089afb33cdbc478e202d3d - - path: results/variant_calling/mutect2/sample2/sample2.mutect2.vcf.gz.tbi - # binary changes md5sums on reruns. - - path: results/mutect2 - should_exist: false -- name: Run variant calling on somatic sample with msisensor-pro - command: nextflow run main.nf -profile test,tools_somatic --tools msisensorpro - tags: - - msisensorpro - - somatic - - variant_calling - files: - - path: results/multiqc - - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3 - - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3_dis - - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3_germline - - path: results/variant_calling/msisensorpro/sample4_vs_sample3/sample4_vs_sample3_somatic - - path: results/msisensorpro - should_exist: false -- name: Run variant calling on germline sample with strelka - command: nextflow run main.nf -profile test,tools_germline --tools strelka - 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 - md5sum: fa17527ede69d65762bd78fe86fbe50a - - 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 - md5sum: f01534408c3a87893b523de5f39deb0b - - 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 -- name: Run variant calling on germline sample with strelka without intervals - command: nextflow run main.nf -profile test,tools_germline --tools strelka --no_intervals - 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 - md5sum: 90bd53c11222b5e07b4b37cbefa0e2d6 - - 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 - md5sum: fd8e449a715922e24fe4ea9c89870432 - - 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 -- name: Run variant calling on tumor only sample with strelka - command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka - tags: - - strelka - - tumor_only - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: 8d2a5e0ad12781c99e773b828e478d35 - - path: results/multiqc - - path: results/reports/bcftools/strelka/sample2/sample2.strelka.variants.bcftools_stats.txt - md5sum: 93bf8f09d155e69418fff988e76cbc1d - - 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", "72 458 47880 0.00956558 6 20 0.3", "314 463 47899 0.00966617 1 1 1"] - - 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/strelka - should_exist: false -- name: Run variant calling on tumor only sample with strelka without intervals - command: nextflow run main.nf -profile test,tools_tumoronly --tools strelka --no_intervals - tags: - - no_intervals - - strelka - - tumor_only - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: 8d2a5e0ad12781c99e773b828e478d35 - - 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/sample2/sample2.strelka.variants.bcftools_stats.txt - md5sum: 9c3427ef0a28c43cc10537974f4bd9c4 - - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.FILTER.summary - md5sum: d1dcce19d82ced016724ace746e95d01 - - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.TsTv.count - md5sum: 9de35bbe9ebe45166b6bd195717f733a - - path: results/reports/vcftools/strelka/sample2/sample2.strelka.variants.TsTv.qual - md5sum: d2908c6821e5f45146a382625e4704c9 - - 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/strelka - should_exist: false -- name: Run variant calling on somatic sample with strelka - command: nextflow run main.nf -profile test,tools_somatic --tools strelka - 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 - md5sum: af8f05fd8a09e96c4c8850b6ef44729e - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt - md5sum: 6cf7a55bcb53b400ce7df7e72c892574 - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt - md5sum: 7cc6f2412d6b3d8e84ec0daece3d5443 - - 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 - md5sum: f01534408c3a87893b523de5f39deb0b - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: c949f848859f138731898aac64a73eaf - - 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 -- name: Run variant calling on somatic sample with strelka without intervals - command: nextflow run main.nf -profile test,tools_somatic --tools strelka --no_intervals - 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 - md5sum: 572bc880d2bf64a00c8f86567c72f575 - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt - md5sum: 6cf7a55bcb53b400ce7df7e72c892574 - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt - md5sum: 21b5d06e7e9f34a05b3d7554240f7669 - - 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 - md5sum: fd8e449a715922e24fe4ea9c89870432 - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: 75af7d1b1e5a2f1bdfe5b530e37a6cbb - - 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 -- name: Run variant calling on somatic sample with strelka & manta (StrelkaBP) - command: nextflow run main.nf -profile test,tools_somatic --tools strelka,manta - tags: - - somatic - - strelkabp - - 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 - md5sum: 5a5ce4cf9c5f48801851d40772d3ba4b - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.bcftools_stats.txt - md5sum: baa05f77160e6cd985050790334c91e8 - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.bcftools_stats.txt - md5sum: 56c39772dc25e451d8209f608bb16e37 - - path: results/reports/bcftools/strelka/sample3/sample3.strelka.variants.bcftools_stats.txt - md5sum: af8f05fd8a09e96c4c8850b6ef44729e - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt - md5sum: 6cf7a55bcb53b400ce7df7e72c892574 - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt - md5sum: 7cc6f2412d6b3d8e84ec0daece3d5443 - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: f01534408c3a87893b523de5f39deb0b - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: c949f848859f138731898aac64a73eaf - - 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: e7ca7e9fe76ce12198fd54ec9a64fad4 - - 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: e7ca7e9fe76ce12198fd54ec9a64fad4 - - 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: e7ca7e9fe76ce12198fd54ec9a64fad4 - - 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 -- name: Run variant calling on somatic sample with & manta (StrelkaBP) without intervals - command: nextflow run main.nf -profile test,tools_somatic --tools strelka,manta --no_intervals - tags: - - no_intervals - - somatic - - strelkabp - - 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 - md5sum: 5a5ce4cf9c5f48801851d40772d3ba4b - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.diploid_sv.bcftools_stats.txt - md5sum: baa05f77160e6cd985050790334c91e8 - - path: results/reports/bcftools/manta/sample4_vs_sample3/sample4_vs_sample3.manta.somatic_sv.bcftools_stats.txt - md5sum: 56c39772dc25e451d8209f608bb16e37 - - path: results/reports/bcftools/strelka/sample3/sample3.strelka.variants.bcftools_stats.txt - md5sum: 572bc880d2bf64a00c8f86567c72f575 - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_indels.bcftools_stats.txt - md5sum: 6cf7a55bcb53b400ce7df7e72c892574 - - path: results/reports/bcftools/strelka/sample4_vs_sample3/sample4_vs_sample3.strelka.somatic_snvs.bcftools_stats.txt - md5sum: 21b5d06e7e9f34a05b3d7554240f7669 - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: fd8e449a715922e24fe4ea9c89870432 - - 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 - md5sum: bc68ae4e688e9fb772b457069e604883 - - 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 - md5sum: 75af7d1b1e5a2f1bdfe5b530e37a6cbb - - 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 -- name: Run variant calling on somatic sample with tiddit - command: nextflow run main.nf -profile test,tools_somatic --tools tiddit - tags: - - tiddit - - somatic - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: 76b499e35c128d67b0606ea561bf70e0 - - path: results/multiqc - - path: results/reports/bcftools/tiddit/sample3/sample3.tiddit.bcftools_stats.txt - md5sum: 47af91809c214102f723a7c58e9b8e72 - - path: results/reports/bcftools/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.bcftools_stats.txt - md5sum: c071ebe8222acd2c76fc019838e8c230 - - path: results/reports/vcftools/tiddit/sample3/sample3.tiddit.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/tiddit/sample3/sample3.tiddit.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/tiddit/sample3/sample3.tiddit.TsTv.qual - md5sum: bc68ae4e688e9fb772b457069e604883 - - path: results/reports/vcftools/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.TsTv.count - md5sum: 8dcfdbcaac118df1d5ad407dd2af699f - - path: results/reports/vcftools/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.TsTv.qual - md5sum: bc68ae4e688e9fb772b457069e604883 - - path: results/variant_calling/tiddit/sample3/sample3.tiddit.ploidies.tab - md5sum: d65f8aa5bb136f77c23264640481f047 - - path: results/variant_calling/tiddit/sample3/sample3.tiddit.vcf.gz - md5sum: 1aeb97037b73251bb79e48b355026c9d - - path: results/variant_calling/tiddit/sample3/sample3.tiddit.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.normal.vcf.gz - md5sum: 5ba8e30a9d831c05e31300b7d2c578ef - - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.normal.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.ploidies.tab - md5sum: d65f8aa5bb136f77c23264640481f047 - - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.tumor.vcf.gz - md5sum: 302cb980260b313573cf53067fd11120 - - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit.tumor.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/variant_calling/tiddit/sample4_vs_sample3/sample4_vs_sample3.tiddit_sv_merge.vcf.gz - md5sum: f69f1fb9c246ac3bbc9270a2ea979557 - - path: results/tiddit - should_exist: false -- name: Run variant calling on germline sample with tiddit - command: nextflow run main.nf -profile test,tools_germline --tools tiddit - tags: - - tiddit - - germline - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: cd458ebee25e1fb1258d2f390e54c736 - - path: results/multiqc - - path: results/reports/bcftools/tiddit/sample1/sample1.tiddit.bcftools_stats.txt - md5sum: 6bde7b353b927f8e99f5d0f3b592e67b - - path: results/reports/vcftools/tiddit/sample1/sample1.tiddit.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/tiddit/sample1/sample1.tiddit.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/tiddit/sample1/sample1.tiddit.TsTv.qual - md5sum: bc68ae4e688e9fb772b457069e604883 - - path: results/variant_calling/tiddit/sample1/sample1.tiddit.ploidies.tab - md5sum: d65f8aa5bb136f77c23264640481f047 - - path: results/variant_calling/tiddit/sample1/sample1.tiddit.vcf.gz - md5sum: 72cd7a6dc9dece29fdcb0a19f69e1cb5 - - path: results/variant_calling/tiddit/sample1/sample1.tiddit.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/tiddit - should_exist: false -- name: Run variant calling on tumor_only sample with tiddit - command: nextflow run main.nf -profile test,tools_tumoronly --tools tiddit - tags: - - tiddit - - tumor_only - - variant_calling - files: - - path: results/csv/variantcalled.csv - md5sum: 15076bb78912fe51006e83934c376fc2 - - path: results/multiqc - - path: results/reports/bcftools/tiddit/sample2/sample2.tiddit.bcftools_stats.txt - md5sum: f2e3a2944f28287286f526d069d473e4 - - path: results/reports/vcftools/tiddit/sample2/sample2.tiddit.FILTER.summary - md5sum: 1ce42d34e4ae919afb519efc99146423 - - path: results/reports/vcftools/tiddit/sample2/sample2.tiddit.TsTv.count - md5sum: fa27f678965b7cba6a92efcd039f802a - - path: results/reports/vcftools/tiddit/sample2/sample2.tiddit.TsTv.qual - md5sum: bc68ae4e688e9fb772b457069e604883 - - path: results/variant_calling/tiddit/sample2/sample2.tiddit.ploidies.tab - md5sum: 0f01874e20df10ecc7418d4537c7aa82 - - path: results/variant_calling/tiddit/sample2/sample2.tiddit.vcf.gz - md5sum: d75c2688964d79a87d882a8ac9a9a93b - - path: results/variant_calling/tiddit/sample2/sample2.tiddit.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - - path: results/tiddit - should_exist: false diff --git a/tests/test_tools_manually.yml b/tests/test_tools_manually.yml index 833b1f8629..a751d7b706 100644 --- a/tests/test_tools_manually.yml +++ b/tests/test_tools_manually.yml @@ -34,7 +34,6 @@ md5sum: 4ac774bf5f1157e77426fd82f5a03013 - path: results/variant_calling/ascat/sample4_vs_sample3/sample4_vs_sample3.tumour_tumourLogR.txt md5sum: c6ef56244b8ac53d2c949437918523b2 - - name: Run variant calling on somatic sample with mutect2 without intervals command: nextflow run main.nf -profile test,tools_somatic --tools mutect2 --no_intervals tags: @@ -87,7 +86,6 @@ md5sum: 17d2091015d04cbd4a26b7a67dc659e6 - path: results/variant_calling/mutect2/sample4_vs_sample3/sample4_vs_sample3.mutect2.vcf.gz.tbi # binary changes md5sums on reruns. - - name: Run variant calling on somatic sample with mutect2 command: nextflow run main.nf -profile test,tools_somatic --tools mutect2 tags: diff --git a/tests/test_trimming.yml b/tests/test_trimming.yml deleted file mode 100644 index fd7ae1c79f..0000000000 --- a/tests/test_trimming.yml +++ /dev/null @@ -1,55 +0,0 @@ -- name: Run trimming pipeline - command: nextflow run main.nf -profile test,trimming --save_trimmed - tags: - - trimming - - preprocessing - files: - - path: results/csv/markduplicates.csv - md5sum: 0d6120bb99e92f6810343270711ca53e - - path: results/csv/markduplicates_no_table.csv - md5sum: 2a2d3d4842befd4def39156463859ee3 - - path: results/csv/recalibrated.csv - md5sum: 2d29d9e53894dcce96a1b5beb6ef3312 - - path: results/multiqc - - path: results/preprocessing/fastp/test/test-test_L1_1.fastp.fastq.gz - md5sum: 325acd143b6fcbf92ca9e34f97d87158 - - path: results/preprocessing/fastp/test/test-test_L1_2.fastp.fastq.gz - md5sum: af73322b9742bce0dd7f767c5c676c0e - - 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: 766a4cd88d3d085c19d8e31540040ecd - - 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/fastp/test - - path: results/reports/fastqc/test-test_L1 - - path: results/reports/markduplicates/test/test.md.cram.metrics - contains: ["test 8304 930 80 523308 3813 0 0 0.375148", "1.0 930 930"] - - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt - md5sum: 626d5c03a6192283a302bde72415c693 - - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt - md5sum: 4a82e0e19a549edae27fc0cc71f6546f - - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt - md5sum: 51e054d8b3b4ef745c94fbda7a2ef2f3 - - path: results/reports/mosdepth/test/test.md.regions.bed.gz - md5sum: 80738b824b3a7d00bdad2d8e26ac3ccc - - path: results/reports/mosdepth/test/test.md.regions.bed.gz.csi - md5sum: a5ad8f917979f62eacfff1461529dbaa - - path: results/reports/mosdepth/test/test.recal.mosdepth.global.dist.txt - md5sum: 626d5c03a6192283a302bde72415c693 - - path: results/reports/mosdepth/test/test.recal.mosdepth.region.dist.txt - md5sum: 4a82e0e19a549edae27fc0cc71f6546f - - path: results/reports/mosdepth/test/test.recal.mosdepth.summary.txt - md5sum: 51e054d8b3b4ef745c94fbda7a2ef2f3 - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz - md5sum: 80738b824b3a7d00bdad2d8e26ac3ccc - - path: results/reports/mosdepth/test/test.recal.regions.bed.gz.csi - md5sum: a5ad8f917979f62eacfff1461529dbaa - - path: results/reports/samtools/test/test.md.cram.stats - md5sum: 7382e028335a2b057cb54ea160c4be7b - - path: results/reports/samtools/test/test.recal.cram.stats - md5sum: 5adeae7e9ce068009e88bacba549096e diff --git a/tests/test_umi.yml b/tests/test_umi.yml index b1d2b5b62d..5ddacea421 100644 --- a/tests/test_umi.yml +++ b/tests/test_umi.yml @@ -1,6 +1,7 @@ - name: Run UMI test command: nextflow run main.nf -profile test,umi tags: + - preprocessing - umi files: - path: results/preprocessing/umi/test/test-test_L1_umi-consensus.bam