X-Git-Url: https://git.arvados.org/arvados-tutorial.git/blobdiff_plain/611c455f8a94ab5dbd5c94415802b5c7fd009ffc..c604c42bb92a6301b13a250582eabed509adaae1:/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..0b6c102 100644
--- a/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
+++ b/WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.cwl
@@ -25,7 +25,7 @@ inputs:
     format: edam:format_2572 # BAM
     label: Recalibrated BAM for given interval
     secondaryFiles:
-      - .bai
+      - ^.bai
   reference:
     type: File
     format: edam:format_1929 # FASTA
@@ -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"