Adding modified code to select variants and gather arrays

[arvados-tutorial.git] / cwl / helper / gatk-selectvariants.cwl

diff --git a/cwl/helper/gatk-selectvariants.cwl b/cwl/helper/gatk-selectvariants.cwl
index 2a65e5340e933f908c951bdf29672da6b6bd4f54..66b5d5c0bb552cb89237881dbd54a41dff198e76 100644 (file)
--- a/cwl/helper/gatk-selectvariants.cwl
+++ b/cwl/helper/gatk-selectvariants.cwl
@@ -35,10 +35,10 @@ inputs:
   sample: string
 
 outputs:
-  genotypegvcf:
+  filteredgvcf:
     type: File
     outputBinding:
-      glob: "*selected.g.vcf.gz"
+      glob: "*g.vcf.gz"
 
 baseCommand: /gatk/gatk
 
@@ -51,6 +51,6 @@ arguments:
   - prefix: "--remove-unused-alternates"
     valueFrom: "true"
   - prefix: "-V"
-    valueFrom: $(inputs.gvcf)
+    valueFrom: $(inputs.gvcf.path)
   - prefix: "-O"
-    valueFrom: $(inputs.sample)selected.g.vcf.gz
+    valueFrom: selected$(inputs.gvcf.basename)