From: Sarah Wait Zaranek <swz@curii.com>
Date: Mon, 27 Jul 2020 20:05:28 +0000 (+0000)
Subject: Fixing labels for knownsites
X-Git-Url: https://git.arvados.org/arvados-tutorial.git/commitdiff_plain/37c7841cd802e86ef51046b56331c1fd39b9a853

Fixing labels for knownsites
Arvados-DCO-1.1-Signed-off-by: Sarah Wait Zaranek <swz@curii.com>
no issue #
---

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: