From 1d795a5a4da543c71213028a8798d39ea06c4c52 Mon Sep 17 00:00:00 2001 From: Rike Date: Tue, 3 May 2022 09:19:20 +0200 Subject: [PATCH 01/13] Add skip germline closes issue #509 --- workflows/sarek.nf | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index eb34bcc8b3..d235cb7be3 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -627,6 +627,22 @@ workflow SAREK { // and remove patient ID field & null value for further processing [meta1, [cram1,crai1]] [meta2, [cram2,crai2]] cram_variant_calling_tumor_only = cram_variant_calling_tumor_filtered.transpose().map{ it -> [it[1], it[2], it[3]] } + if(params.skip_germline_for_somatic){ + // Normal only samples + + // 1. Join with tumor samples, in each channel there is one key per patient now. Patients without matched tumor end up with: [patient1, [meta1], [cram1,crai1], null] as there is only one matched normal possible + cram_variant_calling_normal_joined = cram_variant_calling_normal_to_cross.join(cram_variant_calling_tumor_grouped, remainder: true) + + // 2. Filter out entries with last entry null + cram_variant_calling_normal_filtered = cram_variant_calling_normal_joined.filter{ it -> !(it.last()) } + + // 3. Remove patient ID field & null value for further processing [meta1, [cram1,crai1]] [meta2, [cram2,crai2]] (no transposing needed since only one normal per patient ID) + cram_variant_calling_status_normal = cram_variant_calling_normal_filtered.map{ it -> [it[1], it[2], it[3]] } + + }else{ + cram_variant_calling_status_normal = cram_variant_calling_status.normal + } + // Tumor - normal pairs // Use cross to combine normal with all tumor samples, i.e. multi tumor samples from recurrences cram_variant_calling_pair = cram_variant_calling_normal_to_cross.cross(cram_variant_calling_pair_to_cross) @@ -641,9 +657,11 @@ workflow SAREK { [meta, normal[2], normal[3], tumor[2], tumor[3]] } + //cram_variant_calling_status.normal.view() + // GERMLINE VARIANT CALLING GERMLINE_VARIANT_CALLING( - cram_variant_calling_status.normal, + cram_variant_calling_status_normal, dbsnp, dbsnp_tbi, dict, From d949c8442e11892f6ae8aeba3d9e36204ef4278a Mon Sep 17 00:00:00 2001 From: Rike Date: Tue, 3 May 2022 09:31:35 +0200 Subject: [PATCH 02/13] Add --skip_germline_for_somatic param --- nextflow.config | 1 + nextflow_schema.json | 28 ++++++++++++++++++++++++---- 2 files changed, 25 insertions(+), 4 deletions(-) diff --git a/nextflow.config b/nextflow.config index 638b60ef96..a9f4b40cdf 100644 --- a/nextflow.config +++ b/nextflow.config @@ -27,6 +27,7 @@ params { target_bed = null // No default TargetBED file for targeted sequencing tools = null // No default Variant_Calling or Annotation tools skip_tools = null // All tools (markduplicates + baserecalibrator + QC) are used by default + skip_germline_for_somatic = false // Modify fastqs (trim/split) trim_fastq = false // No trimming diff --git a/nextflow_schema.json b/nextflow_schema.json index 0f4f600dc4..6f0e1c772a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,7 +10,11 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": ["step", "input", "outdir"], + "required": [ + "step", + "input", + "outdir" + ], "properties": { "step": { "type": "string", @@ -198,7 +202,11 @@ "type": "string", "default": "bwa-mem", "fa_icon": "fas fa-puzzle-piece", - "enum": ["bwa-mem", "bwa-mem2", "dragmap"], + "enum": [ + "bwa-mem", + "bwa-mem2", + "dragmap" + ], "description": "Specify aligner to be used to map reads to reference genome.", "help_text": "> **WARNING** Current indices for `bwa` in AWS iGenomes are not compatible with `bwa-mem2` and `dragmap`.\n> Use `--bwa=false` to have `Sarek` build them automatically.\n\n> **WARNING** BWA-mem2 is in active development\n> Sarek might not be able to require the right amount of resources for it at the moment\n> We recommend to use pre-built indexes", "hidden": true @@ -232,6 +240,11 @@ "default": "", "fa_icon": "fas fa-toolbox", "properties": { + "skip_germline_for_somatic": { + "type": "boolean", + "fa_icon": "fas fa-angle-double-right", + "description": "If true, skips germline variant calling for matched normal to tumor sample. Normal samples without matched tumor will still be processed through germline variant calling tools." + }, "ploidy": { "type": "number", "fa_icon": "fas fa-bacon", @@ -665,7 +678,14 @@ "description": "Method used to save pipeline results to output directory.", "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", "fa_icon": "fas fa-copy", - "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], + "enum": [ + "symlink", + "rellink", + "link", + "copy", + "copyNoFollow", + "move" + ], "hidden": true }, "email": { @@ -776,4 +796,4 @@ "$ref": "#/definitions/generic_options" } ] -} +} \ No newline at end of file From 0c242bc7077ebc6cd2de662025580b7650a29625 Mon Sep 17 00:00:00 2001 From: Rike Date: Tue, 3 May 2022 09:49:56 +0200 Subject: [PATCH 03/13] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0d1499919b..2148ef1f02 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#507](https://github.com/nf-core/sarek/pull/507) - Subway map for building indexes - [#512](https://github.com/nf-core/sarek/pull/512) - Subway map for pipeline - [#522](https://github.com/nf-core/sarek/pull/522) - Add QC for vcf files & MultiQC +- [#533](https://github.com/nf-core/sarek/pull/533) - Add param `--skip_germline_for_somatic` to allow skipping of germline variantcalling for paired samples ### Changed From db38c19b686717909c2b817d68de0b33a90f25d7 Mon Sep 17 00:00:00 2001 From: Rike Date: Tue, 3 May 2022 13:34:55 +0200 Subject: [PATCH 04/13] Prettier --- nextflow_schema.json | 23 ++++------------------- 1 file changed, 4 insertions(+), 19 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 6f0e1c772a..6a6a9fe4df 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -10,11 +10,7 @@ "type": "object", "fa_icon": "fas fa-terminal", "description": "Define where the pipeline should find input data and save output data.", - "required": [ - "step", - "input", - "outdir" - ], + "required": ["step", "input", "outdir"], "properties": { "step": { "type": "string", @@ -202,11 +198,7 @@ "type": "string", "default": "bwa-mem", "fa_icon": "fas fa-puzzle-piece", - "enum": [ - "bwa-mem", - "bwa-mem2", - "dragmap" - ], + "enum": ["bwa-mem", "bwa-mem2", "dragmap"], "description": "Specify aligner to be used to map reads to reference genome.", "help_text": "> **WARNING** Current indices for `bwa` in AWS iGenomes are not compatible with `bwa-mem2` and `dragmap`.\n> Use `--bwa=false` to have `Sarek` build them automatically.\n\n> **WARNING** BWA-mem2 is in active development\n> Sarek might not be able to require the right amount of resources for it at the moment\n> We recommend to use pre-built indexes", "hidden": true @@ -678,14 +670,7 @@ "description": "Method used to save pipeline results to output directory.", "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", "fa_icon": "fas fa-copy", - "enum": [ - "symlink", - "rellink", - "link", - "copy", - "copyNoFollow", - "move" - ], + "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "hidden": true }, "email": { @@ -796,4 +781,4 @@ "$ref": "#/definitions/generic_options" } ] -} \ No newline at end of file +} From e1b61d76586c39c5e8e59ba0361606b1330e1f1b Mon Sep 17 00:00:00 2001 From: Rike Date: Tue, 3 May 2022 13:52:36 +0200 Subject: [PATCH 05/13] rename parameter after code review --- nextflow.config | 2 +- nextflow_schema.json | 2 +- workflows/sarek.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/nextflow.config b/nextflow.config index a9f4b40cdf..8dbbb69937 100644 --- a/nextflow.config +++ b/nextflow.config @@ -27,7 +27,6 @@ params { target_bed = null // No default TargetBED file for targeted sequencing tools = null // No default Variant_Calling or Annotation tools skip_tools = null // All tools (markduplicates + baserecalibrator + QC) are used by default - skip_germline_for_somatic = false // Modify fastqs (trim/split) trim_fastq = false // No trimming @@ -52,6 +51,7 @@ params { sequencing_center = null // No sequencing center to be written in BAM header by aligner // Variant Calling + only_paired_variant_calling = false //if true, skips germline variant calling for normal-paired samples ploidy = 2 //null (in ascat, test this works) // Use default value, you can use 2,3,4 ascat_purity = null // Use default value cf_coeff = 0.05 // default value for Control-FREEC diff --git a/nextflow_schema.json b/nextflow_schema.json index 6a6a9fe4df..5995db9b7a 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -232,7 +232,7 @@ "default": "", "fa_icon": "fas fa-toolbox", "properties": { - "skip_germline_for_somatic": { + "only_paired_variant_calling": { "type": "boolean", "fa_icon": "fas fa-angle-double-right", "description": "If true, skips germline variant calling for matched normal to tumor sample. Normal samples without matched tumor will still be processed through germline variant calling tools." diff --git a/workflows/sarek.nf b/workflows/sarek.nf index d235cb7be3..132c3e47dd 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -627,7 +627,7 @@ workflow SAREK { // and remove patient ID field & null value for further processing [meta1, [cram1,crai1]] [meta2, [cram2,crai2]] cram_variant_calling_tumor_only = cram_variant_calling_tumor_filtered.transpose().map{ it -> [it[1], it[2], it[3]] } - if(params.skip_germline_for_somatic){ + if(params.only_paired_variant_calling){ // Normal only samples // 1. Join with tumor samples, in each channel there is one key per patient now. Patients without matched tumor end up with: [patient1, [meta1], [cram1,crai1], null] as there is only one matched normal possible From b74669ac43b0611ab8570f9da892a4965f1d99e8 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Tue, 3 May 2022 15:57:16 +0200 Subject: [PATCH 06/13] Update CHANGELOG.md Co-authored-by: Maxime U. Garcia --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2148ef1f02..264bf4de0f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -21,7 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#507](https://github.com/nf-core/sarek/pull/507) - Subway map for building indexes - [#512](https://github.com/nf-core/sarek/pull/512) - Subway map for pipeline - [#522](https://github.com/nf-core/sarek/pull/522) - Add QC for vcf files & MultiQC -- [#533](https://github.com/nf-core/sarek/pull/533) - Add param `--skip_germline_for_somatic` to allow skipping of germline variantcalling for paired samples +- [#533](https://github.com/nf-core/sarek/pull/533) - Add param `--only_paired_variant_calling` to allow skipping of germline variantcalling for paired samples ### Changed From c5ebdd19e55d7d2882933024827587db25fe6f1e Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Tue, 3 May 2022 16:35:56 +0200 Subject: [PATCH 07/13] Update workflows/sarek.nf --- workflows/sarek.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index 132c3e47dd..d097217738 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -657,7 +657,6 @@ workflow SAREK { [meta, normal[2], normal[3], tumor[2], tumor[3]] } - //cram_variant_calling_status.normal.view() // GERMLINE VARIANT CALLING GERMLINE_VARIANT_CALLING( From 088b18b65f4ab49abbfd2134c10060ec999b0b0b Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Tue, 3 May 2022 16:36:11 +0200 Subject: [PATCH 08/13] Update workflows/sarek.nf --- workflows/sarek.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/workflows/sarek.nf b/workflows/sarek.nf index d097217738..d793c6f76d 100644 --- a/workflows/sarek.nf +++ b/workflows/sarek.nf @@ -657,7 +657,6 @@ workflow SAREK { [meta, normal[2], normal[3], tumor[2], tumor[3]] } - // GERMLINE VARIANT CALLING GERMLINE_VARIANT_CALLING( cram_variant_calling_status_normal, From 33fe375982d1a0e831dc3513ee0f0e79c8481e3f Mon Sep 17 00:00:00 2001 From: Rike Date: Tue, 3 May 2022 17:47:32 +0200 Subject: [PATCH 09/13] Add single sample tests --- .github/workflows/ci.yml | 1 + tests/test_only_paired_VC.yml | 22 ++++++++++++++++++++++ 2 files changed, 23 insertions(+) create mode 100644 tests/test_only_paired_VC.yml diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 16dc1a4458..a6a44ca454 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -43,6 +43,7 @@ jobs: - "mutect2" - "msisensorpro" # - 'save_bam_mapped' + - "single_sample" - "skip_markduplicates" - "strelka" - "split_fastq" diff --git a/tests/test_only_paired_VC.yml b/tests/test_only_paired_VC.yml new file mode 100644 index 0000000000..e098087b8c --- /dev/null +++ b/tests/test_only_paired_VC.yml @@ -0,0 +1,22 @@ +- name: Run variant calling on germline sample with strelka + command: nextflow run main.nf -profile test,tools_somatic,docker --tools strelka --only_paired_variant_calling + tags: + - somatic + - strelka + - variant_calling + - single_sample + files: + - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz + should_exist: false + - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz.tbi + should_exist: false + - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz + should_exist: false + - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz.tbi + should_exist: false + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz.tbi +# Add test for mixed normal-paired, normal-single +# Add test for tumor-single From d4a9d0479755716e03166c0babb0799d8129da95 Mon Sep 17 00:00:00 2001 From: Rike Date: Tue, 3 May 2022 18:36:27 +0200 Subject: [PATCH 10/13] Fix test naming --- tests/test_only_paired_VC.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_only_paired_VC.yml b/tests/test_only_paired_VC.yml index e098087b8c..051fa112df 100644 --- a/tests/test_only_paired_VC.yml +++ b/tests/test_only_paired_VC.yml @@ -1,4 +1,4 @@ -- name: Run variant calling on germline sample with strelka +- name: Skip variant calling on matched normal command: nextflow run main.nf -profile test,tools_somatic,docker --tools strelka --only_paired_variant_calling tags: - somatic From 4872222d5734bbebdd730ec70004fb93cd348622 Mon Sep 17 00:00:00 2001 From: Rike Date: Tue, 3 May 2022 22:19:19 +0200 Subject: [PATCH 11/13] Add tests for varaint calling channel magic --- .github/workflows/ci.yml | 2 +- conf/test.config | 7 +++++ tests/csv/3.0/variantcalling_channels.csv | 5 ++++ tests/test_only_paired_VC.yml | 31 ++++++++++++++++++++--- 4 files changed, 40 insertions(+), 5 deletions(-) create mode 100644 tests/csv/3.0/variantcalling_channels.csv diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a6a44ca454..be4b5d033a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -43,7 +43,7 @@ jobs: - "mutect2" - "msisensorpro" # - 'save_bam_mapped' - - "single_sample" + - "variantcalling_channel" - "skip_markduplicates" - "strelka" - "split_fastq" diff --git a/conf/test.config b/conf/test.config index 57884bd794..58c051472f 100644 --- a/conf/test.config +++ b/conf/test.config @@ -139,6 +139,13 @@ profiles { use_gatk_spark { params.use_gatk_spark = 'baserecalibrator,markduplicates' } + variantcalling_channels { + params.input = "${baseDir}/tests/csv/3.0/variantcalling_channels.csv" + params.fasta = "${params.genomes_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" + params.wes = true + params.step = 'variant_calling' + params.intervals = "${params.genomes_base}/data/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" + } } //This is apparently useless as it won't overwrite things in the modules.config diff --git a/tests/csv/3.0/variantcalling_channels.csv b/tests/csv/3.0/variantcalling_channels.csv new file mode 100644 index 0000000000..17d912e966 --- /dev/null +++ b/tests/csv/3.0/variantcalling_channels.csv @@ -0,0 +1,5 @@ +patient,gender,status,sample,cram,crai +test,XX,0,sample1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai +test1,XX,1,sample2,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai +test3,XX,0,sample3,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai +test3,XX,1,sample4,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai diff --git a/tests/test_only_paired_VC.yml b/tests/test_only_paired_VC.yml index 051fa112df..1f8c67f93e 100644 --- a/tests/test_only_paired_VC.yml +++ b/tests/test_only_paired_VC.yml @@ -1,10 +1,10 @@ - name: Skip variant calling on matched normal - command: nextflow run main.nf -profile test,tools_somatic,docker --tools strelka --only_paired_variant_calling + command: nextflow run main.nf -profile test,variantcalling_channels,docker --tools strelka --only_paired_variant_calling tags: - somatic - strelka - variant_calling - - single_sample + - variantcalling_channel files: - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz should_exist: false @@ -14,9 +14,32 @@ should_exist: false - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz.tbi should_exist: false + - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz + - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz.tbi + - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz + - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz.tbi + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz + - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz.tbi + +- name: Do germline variant calling on matched normal + command: nextflow run main.nf -profile test,variantcalling_channels,docker --tools strelka + tags: + - somatic + - strelka + - variant_calling + - variantcalling_channel + files: + - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz + - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz.tbi + - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz + - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz.tbi + - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz + - path: results/variant_calling/sample2/strelka/sample2.variants.vcf.gz.tbi + - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz + - path: results/variant_calling/sample2/strelka/sample2.genome.vcf.gz.tbi - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_indels.vcf.gz.tbi - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz - path: results/variant_calling/sample4_vs_sample3/strelka/sample4_vs_sample3.somatic_snvs.vcf.gz.tbi -# Add test for mixed normal-paired, normal-single -# Add test for tumor-single From b257ac38faf88ae1e233fdd2fb413f1f5765356f Mon Sep 17 00:00:00 2001 From: Rike Date: Wed, 4 May 2022 10:24:04 +0200 Subject: [PATCH 12/13] Add paths for single normal sample --- tests/test_only_paired_VC.yml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/tests/test_only_paired_VC.yml b/tests/test_only_paired_VC.yml index 1f8c67f93e..6c67407385 100644 --- a/tests/test_only_paired_VC.yml +++ b/tests/test_only_paired_VC.yml @@ -6,6 +6,10 @@ - variant_calling - variantcalling_channel files: + - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz + - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz.tbi + - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz + - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz.tbi - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz should_exist: false - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz.tbi @@ -31,6 +35,10 @@ - variant_calling - variantcalling_channel files: + - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz + - path: results/variant_calling/sample1/strelka/sample1.variants.vcf.gz.tbi + - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz + - path: results/variant_calling/sample1/strelka/sample1.genome.vcf.gz.tbi - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz - path: results/variant_calling/sample3/strelka/sample3.variants.vcf.gz.tbi - path: results/variant_calling/sample3/strelka/sample3.genome.vcf.gz From e3868b45f413721f5b76defc408286d46bc0e7d1 Mon Sep 17 00:00:00 2001 From: Rike Date: Wed, 4 May 2022 11:28:57 +0200 Subject: [PATCH 13/13] Replcae new csv with recalibrated.csv to recycle more --- conf/test.config | 2 +- tests/csv/3.0/variantcalling_channels.csv | 5 ----- 2 files changed, 1 insertion(+), 6 deletions(-) delete mode 100644 tests/csv/3.0/variantcalling_channels.csv diff --git a/conf/test.config b/conf/test.config index 58c051472f..43010f4096 100644 --- a/conf/test.config +++ b/conf/test.config @@ -140,7 +140,7 @@ profiles { params.use_gatk_spark = 'baserecalibrator,markduplicates' } variantcalling_channels { - params.input = "${baseDir}/tests/csv/3.0/variantcalling_channels.csv" + params.input = "${baseDir}/tests/csv/3.0/recalibrated.csv" params.fasta = "${params.genomes_base}/data/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta" params.wes = true params.step = 'variant_calling' diff --git a/tests/csv/3.0/variantcalling_channels.csv b/tests/csv/3.0/variantcalling_channels.csv deleted file mode 100644 index 17d912e966..0000000000 --- a/tests/csv/3.0/variantcalling_channels.csv +++ /dev/null @@ -1,5 +0,0 @@ -patient,gender,status,sample,cram,crai -test,XX,0,sample1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai -test1,XX,1,sample2,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai -test3,XX,0,sample3,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai -test3,XX,1,sample4,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai