Switching variable knownsites1 to knownsites

[arvados-tutorial.git] / WGS-processing / cwl / helper / gatk-wf-with-interval.cwl

diff --git a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
index ef902099c066015699866acad47b4129da3ffcc1..38e185d5b67e26f299bb39a4b1419cd5893fd9e8 100644 (file)
--- a/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-wf-with-interval.cwl
@@ -1,6 +1,6 @@
 cwlVersion: v1.1
 class: Workflow
-label: Variant calling workflow for single interval 
+label: Variant calling workflow for given interval 
 
 requirements:
   - class: SubworkflowFeatureRequirement
@@ -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
@@ -41,7 +41,7 @@ outputs:
   gvcf:
     type: File
     format: edam:format_3016 # GVCF
-    label: single interval filtered GVCF
+    label: Given interval filtered GVCF
     outputSource: selectvariants/filteredgvcf
 
 steps:
@@ -51,7 +51,7 @@ steps:
       bam: bam
       reference: reference
       sample: sample
-      knownsites1: knownsites1
+      knownsites: knownsites
       intervallist: intervallist
     out: [recaltable]
   applyBQSR: