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 76e4798bf270315a57d10a2363aa203487feedc1..41c9130e923c35cd86164f404a38db4165225eb4 100644 (file)
--- 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 2de30a62b88d0a0923b6951eaa05b9cf31c0ddc2..ea00e91a5b4d8ce3e93ded400a85927973f37281 100644 (file)
--- 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 d9023c92186ca6fda034cbf4552accdb5c069364..b3ea17f6eefda46ac0616ae4eeee0d4507768d73 100644 (file)
--- 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 13bd4af04c3528e384078e073c4e722823e498ec..7e48e04d135b9640ac64479138cc01d9822149ab 100644 (file)
--- 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: