From 37c7841cd802e86ef51046b56331c1fd39b9a853 Mon Sep 17 00:00:00 2001 From: Sarah Wait Zaranek Date: Mon, 27 Jul 2020 20:05:28 +0000 Subject: [PATCH] Fixing labels for knownsites Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek no issue # --- WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl | 8 ++++---- .../cwl/helper/gatk-baserecalibrator-with-interval.cwl | 4 ++-- WGS-processing/cwl/helper/gatk-wf-with-interval.cwl | 4 ++-- .../cwl/helper/scatter-gatk-wf-with-interval.cwl | 4 ++-- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl index 76e4798..41c9130 100644 --- a/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl +++ b/WGS-processing/cwl/helper/bwamem-gatk-report-wf.cwl @@ -35,15 +35,15 @@ inputs: knownsites1: type: File format: edam:format_3016 # VCF - label: VCF of known polymorphic sites for BQSR + label: VCF of known SNPS sites for BQSR secondaryFiles: - - .idx + - .idx knownsites2: type: File format: edam:format_3016 # VCF - label: VCF of known polymorphic sites for BQSR + label: VCF of known indel sites for BQSR secondaryFiles: - - .tbi + - .tbi scattercount: type: string label: Desired split for variant calling diff --git a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl index 2de30a6..ea00e91 100644 --- a/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl +++ b/WGS-processing/cwl/helper/gatk-baserecalibrator-with-interval.cwl @@ -44,13 +44,13 @@ inputs: knownsites1: type: File format: edam:format_3016 # VCF - label: VCF of known polymorphic sites for BQSR + label: VCF of known SNPS sites for BQSR secondaryFiles: - .idx knownsites2: type: File format: edam:format_3016 # VCF - label: VCF of known polymorphic sites for BQSR + label: VCF of known indel sites for BQSR secondaryFiles: - .tbi intervallist: diff --git a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl index d9023c9..b3ea17f 100644 --- a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl +++ b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl @@ -30,13 +30,13 @@ inputs: knownsites1: type: File format: edam:format_3016 # VCF - label: VCF of known polymorphic sites for BQSR + label: VCF of known SNPS sites for BQSR secondaryFiles: - .idx knownsites2: type: File format: edam:format_3016 # VCF - label: VCF of known polymorphic sites for BQSR + label: VCF of known indel sites for BQSR secondaryFiles: - .tbi intervallist: 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 13bd4af..7e48e04 100644 --- a/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl +++ b/WGS-processing/cwl/helper/scatter-gatk-wf-with-interval.cwl @@ -34,13 +34,13 @@ inputs: knownsites1: type: File format: edam:format_3016 # VCF - label: VCF of known polymorphic sites for BQSR + label: VCF of known SNPS sites for BQSR secondaryFiles: - .idx knownsites2: type: File format: edam:format_3016 # VCF - label: VCF of known polymorphic sites for BQSR + label: VCF of known indel sites for BQSR secondaryFiles: - .tbi scattercount: -- 2.30.2