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Updating yml files
[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..4b3d1a79fc809fbdecccf1cd2da6b17617311680 100644
(file)
--- 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"
- 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"