Updating CWL for overarching workflow

[arvados-tutorial.git] / cwl / bwa-gatk-wf.cwl

diff --git a/cwl/bwa-gatk-wf.cwl b/cwl/bwa-gatk-wf.cwl
index 6e1f326127baf9e2e016bfd2bad1c3c7d0b838ce..56c1758f591f1e02dbe3c145333c771ff81a3fd6 100644 (file)
--- a/cwl/bwa-gatk-wf.cwl
+++ b/cwl/bwa-gatk-wf.cwl
@@ -1,6 +1,9 @@
 cwlVersion: v1.1
 class: Workflow
 
+requirements:
+  - class: SubworkflowFeatureRequirement
+
 inputs:
   fastq1: File
   fastq2: File
@@ -25,7 +28,7 @@ outputs:
     outputSource: fastqc/out-zip 
   vcf:
     type: File
-    outputSource: vep/out-vcf
+    outputSource: haplotypecaller/vcf
 
 steps:
   fastqc: