Bugfix .bai secondary file for ApplyBSQR behavior

[arvados-tutorial.git] / 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 53d7ee209b02d34e59ac96c1cbf34a417dfe28e2..0b6c1029ddc3f135ec39fbb834587906f336ffe3 100644 (file)
--- 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:
     format: edam:format_2572 # BAM
     label: Recalibrated BAM for given interval
     secondaryFiles:

-      - .bai
+      - ^.bai

   reference:
     type: File
     format: edam:format_1929 # FASTA
   reference:
     type: File
     format: edam:format_1929 # FASTA


@@ -68,7 +68,7 @@ arguments:
   - prefix: "-L"
     valueFrom: $(inputs.intervallist)
   - prefix: "-O"
   - 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"
   - prefix: "-ERC"
     valueFrom: "GVCF"
   - prefix: "-GQB"