Adding modified code to select variants and gather arrays

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

diff --git a/cwl/helper/gatk-wf-with-interval.cwl b/cwl/helper/gatk-wf-with-interval.cwl
index 037accdc06db269ae3bc885d2897f58a42671d6b..4e9f456b24fec167cc3098a71560395254dd74da 100644 (file)
--- a/cwl/helper/gatk-wf-with-interval.cwl
+++ b/cwl/helper/gatk-wf-with-interval.cwl
@@ -30,7 +30,7 @@ inputs:
 outputs:
   gvcf:
     type: File
-    outputSource: haplotypecaller/gvcf
+    outputSource: selectvariants/filteredgvcf
 
 steps:
   basecalibrator:
@@ -59,3 +59,10 @@ steps:
       sample: sample
       intervallist: intervallist
     out: [gvcf]
+  selectvariants:
+    run: gatk-selectvariants.cwl
+    in: 
+      gvcf: haplotypecaller/gvcf
+      reference: reference
+      sample: sample
+    out: [filteredgvcf]