X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/b825be9a6707d90363ed45ee151cbaebdce3ff60..62cbf7ae299d16727aeb1a48aba27af9f77a3073:/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl

diff --git a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
index 53d7ee2..4b3d1a7 100644
--- a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
@@ -68,7 +68,7 @@ arguments:
   - prefix: "-L"
     valueFrom: $(inputs.intervallist)
   - prefix: "-O"
-    valueFrom: $(runtime.outdir)/$(inputs.sample)-$(inputs.intervallist.nameroot).gatk.g.vcf.gz
+    valueFrom: $(inputs.sample)-$(inputs.intervallist.nameroot).gatk.g.vcf.gz
   - prefix: "-ERC"
     valueFrom: "GVCF"
   - prefix: "-GQB"