From 48f2b200216c57788577d45e080ab6bae212f90b Mon Sep 17 00:00:00 2001 From: Sarah Wait Zaranek Date: Fri, 3 Jul 2020 13:31:35 +0000 Subject: [PATCH] Removing initial work dir requirement when not needed Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl | 5 +---- .../cwl/helper/gatk-baserecalibrator-with-interval.cwl | 5 +---- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl index d8f6afd..52413a6 100644 --- a/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl +++ b/WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl @@ -5,9 +5,6 @@ label: Apply base quality score recalibration requirements: DockerRequirement: dockerPull: broadinstitute/gatk:4.1.7.0 - InitialWorkDirRequirement: - listing: - - $(inputs.bam) hints: arv:RuntimeConstraints: @@ -70,7 +67,7 @@ arguments: - prefix: "-R" valueFrom: $(inputs.reference) - prefix: "-I" - valueFrom: $(inputs.bam.basename) + valueFrom: $(inputs.bam) - prefix: "--bqsr-recal-file" valueFrom: $(inputs.recaltable) - prefix: "-L" diff --git a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl index 80859e6..7ae0837 100644 --- a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl +++ b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl @@ -5,9 +5,6 @@ label: Generate recalibration table for BQSR requirements: DockerRequirement: dockerPull: broadinstitute/gatk:4.1.7.0 - InitialWorkDirRequirement: - listing: - - $(inputs.bam) hints: arv:RuntimeConstraints: @@ -70,7 +67,7 @@ arguments: - prefix: "-R" valueFrom: $(inputs.reference) - prefix: "-I" - valueFrom: $(inputs.bam.basename) + valueFrom: $(inputs.bam) - prefix: "--known-sites" valueFrom: $(inputs.knownsites) - prefix: "-L" -- 2.30.2