Adding files for gathering gvcfs and cleaning gvcfs

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

diff --git a/cwl/helper/gatk-haplotypecaller-with-interval.cwl b/cwl/helper/gatk-haplotypecaller-with-interval.cwl
index e66c5b5b37631f8613227399356b6fa679e8d9ba..3e0b53d3e53a2a22fb0f7e616b0a78c7316a2aca 100644 (file)
--- a/cwl/helper/gatk-haplotypecaller-with-interval.cwl
+++ b/cwl/helper/gatk-haplotypecaller-with-interval.cwl
@@ -56,7 +56,7 @@ arguments:
   - prefix: "-L"
     valueFrom: $(inputs.intervallist)
   - prefix: "-O"
-    valueFrom: $(runtime.outdir)/$(inputs.sample).gatk.g.vcf.gz
+    valueFrom: $(runtime.outdir)/$(inputs.sample)-$(inputs.intervallist.nameroot).gatk.g.vcf.gz
   - prefix: "-ERC"
     valueFrom: "GVCF"
   - prefix: "-GQB"