From 7a2d69e125ee52fd3a7a6eeca6f673c6a083033e Mon Sep 17 00:00:00 2001 From: Sarah Wait Zaranek Date: Wed, 1 Jul 2020 18:56:55 +0000 Subject: [PATCH] Switching variable knownsites1 to knownsites Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl | 2 +- .../cwl/helper/gatk-baserecalibrator-with-interval.cwl | 4 ++-- WGS-processing/cwl/helper/gatk-wf-with-interval.cwl | 4 ++-- WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl | 4 ++-- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl index 86d1e10..56efe65 100644 --- a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl +++ b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl @@ -113,7 +113,7 @@ steps: bam: samtools-index/indexedbam sample: sample scattercount: scattercount - knownsites1: knownsites + knownsites: knownsites out: [gatheredgvcf] generate-report: run: report-wf.cwl diff --git a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl index 7e5bf4d..6df9de1 100644 --- a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl +++ b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl @@ -44,7 +44,7 @@ inputs: sample: type: string label: Sample Name - knownsites1: + knownsites: type: File format: edam:format_3016 # VCF label: VCF of known polymorphic sites for BQSR @@ -72,7 +72,7 @@ arguments: - prefix: "-I" valueFrom: $(inputs.bam.basename) - prefix: "--known-sites" - valueFrom: $(inputs.knownsites1) + valueFrom: $(inputs.knownsites) - prefix: "-L" valueFrom: $(inputs.intervallist) - prefix: "-O" diff --git a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl index cf815a5..38e185d 100644 --- a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl +++ b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl @@ -27,7 +27,7 @@ inputs: sample: type: string label: Sample Name - knownsites1: + knownsites: type: File format: edam:format_3016 # VCF label: VCF of known polymorphic sites for BQSR @@ -51,7 +51,7 @@ steps: bam: bam reference: reference sample: sample - knownsites1: knownsites1 + knownsites: knownsites intervallist: intervallist out: [recaltable] applyBQSR: diff --git a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl index 45653db..2cf48b5 100644 --- a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl +++ b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl @@ -28,7 +28,7 @@ inputs: sample: type: string label: Sample Name - knownsites1: + knownsites: type: File format: edam:format_3016 # VCF label: VCF of known polymorphic sites for BQSR @@ -63,7 +63,7 @@ steps: bam: bam reference: reference sample: sample - knownsites1: knownsites1 + knownsites: knownsites intervallist: splitintervals/intervalfiles out: [gvcf] -- 2.30.2