From e51be256264b4ee9e14eb9ae21fe69568d3c3940 Mon Sep 17 00:00:00 2001 From: Paul Cantalupo Date: Mon, 13 Jul 2020 11:01:00 -0400 Subject: [PATCH 1/3] added dont_use_soft_clipped_bases option --- main.nf | 3 +++ 1 file changed, 3 insertions(+) diff --git a/main.nf b/main.nf index 59dff44522..4954199528 100644 --- a/main.nf +++ b/main.nf @@ -94,6 +94,7 @@ def helpMessage() { Default: ${params.cf_ploidy} --cf_window [int] Control-FREEC window size Default: Disabled + --dont_use_soft_clipped_bases [bool] Do not analyze soft clipped bases in the reads for GATK Mutect2 --no_gvcf [bool] No g.vcf output from GATK HaplotypeCaller --no_strelka_bp [bool] Will not use Manta candidateSmallIndels for Strelka (not recommended by Best Practices) --pon [file] Panel-of-normals VCF (bgzipped) for GATK Mutect2 / Sentieon TNscope @@ -2465,6 +2466,7 @@ process Mutect2 { // https://gatkforums.broadinstitute.org/gatk/discussion/11136/how-to-call-somatic-mutations-using-gatk4-mutect2 PON = params.pon ? "--panel-of-normals ${pon}" : "" intervalsOptions = params.no_intervals ? "" : "-L ${intervalBed}" + softclippedOption = params.dont_use_soft_clipped_bases ? "--dont-use-soft-clipped-bases true" : "" """ # Get raw calls gatk --java-options "-Xmx${task.memory.toGiga()}g" \ @@ -2473,6 +2475,7 @@ process Mutect2 { -I ${bamTumor} -tumor ${idSampleTumor} \ -I ${bamNormal} -normal ${idSampleNormal} \ ${intervalsOptions} \ + ${softclippedOption} \ --germline-resource ${germlineResource} \ ${PON} \ -O ${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf From bacf83533fce249b86e2141dafccecc0015d3034 Mon Sep 17 00:00:00 2001 From: Paul Cantalupo Date: Mon, 13 Jul 2020 11:28:32 -0400 Subject: [PATCH 2/3] added default value --- nextflow.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nextflow.config b/nextflow.config index d09dd010ab..4c84dca0eb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -66,6 +66,7 @@ params { no_strelka_bp = null // Strelka will use Manta candidateSmallIndels if available pon = false // No default PON (Panel of Normals) file for GATK Mutect2 / Sentieon TNscope pon_index = false // No default PON index for GATK Mutect2 / Sentieon TNscope + dont_use_soft_clipped_bases = null // GATK Mutect2 // Annotation annotate_tools = null // Only with --step annotate From aa0162d019dba66bf0973633bfba236daf835dc5 Mon Sep 17 00:00:00 2001 From: Paul Cantalupo Date: Mon, 13 Jul 2020 12:01:09 -0400 Subject: [PATCH 3/3] Apply suggestions from code review Co-authored-by: Maxime Garcia --- main.nf | 6 +++--- nextflow.config | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/main.nf b/main.nf index 4954199528..91c231ee51 100644 --- a/main.nf +++ b/main.nf @@ -94,7 +94,7 @@ def helpMessage() { Default: ${params.cf_ploidy} --cf_window [int] Control-FREEC window size Default: Disabled - --dont_use_soft_clipped_bases [bool] Do not analyze soft clipped bases in the reads for GATK Mutect2 + --ignore_soft_clipped_bases [bool] Do not analyze soft clipped bases in the reads for GATK Mutect2 --no_gvcf [bool] No g.vcf output from GATK HaplotypeCaller --no_strelka_bp [bool] Will not use Manta candidateSmallIndels for Strelka (not recommended by Best Practices) --pon [file] Panel-of-normals VCF (bgzipped) for GATK Mutect2 / Sentieon TNscope @@ -2466,7 +2466,7 @@ process Mutect2 { // https://gatkforums.broadinstitute.org/gatk/discussion/11136/how-to-call-somatic-mutations-using-gatk4-mutect2 PON = params.pon ? "--panel-of-normals ${pon}" : "" intervalsOptions = params.no_intervals ? "" : "-L ${intervalBed}" - softclippedOption = params.dont_use_soft_clipped_bases ? "--dont-use-soft-clipped-bases true" : "" + softClippedOption = params.ignore_soft_clipped_bases ? "--dont-use-soft-clipped-bases true" : "" """ # Get raw calls gatk --java-options "-Xmx${task.memory.toGiga()}g" \ @@ -2475,7 +2475,7 @@ process Mutect2 { -I ${bamTumor} -tumor ${idSampleTumor} \ -I ${bamNormal} -normal ${idSampleNormal} \ ${intervalsOptions} \ - ${softclippedOption} \ + ${softClippedOption} \ --germline-resource ${germlineResource} \ ${PON} \ -O ${intervalBed.baseName}_${idSampleTumor}_vs_${idSampleNormal}.vcf diff --git a/nextflow.config b/nextflow.config index 4c84dca0eb..c2d00e6510 100644 --- a/nextflow.config +++ b/nextflow.config @@ -66,7 +66,7 @@ params { no_strelka_bp = null // Strelka will use Manta candidateSmallIndels if available pon = false // No default PON (Panel of Normals) file for GATK Mutect2 / Sentieon TNscope pon_index = false // No default PON index for GATK Mutect2 / Sentieon TNscope - dont_use_soft_clipped_bases = null // GATK Mutect2 + ignore_soft_clipped_bases = null // GATK Mutect2 // Annotation annotate_tools = null // Only with --step annotate