format: edam:format_2572 # BAM
label: Recalibrated BAM for given interval
secondaryFiles:
- - .bai
+ - ^.bai
reference:
type: File
format: edam:format_1929 # FASTA
- 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"