ShellCommandRequirement: {}
InitialWorkDirRequirement:
listing:
- - $(inputs.gvcflist)
- $(inputs.gvcf1)
- $(inputs.gvcf2)
type: File
gvcf2:
type: File
- gvcflist:
- type: File
sample: string
reference:
type: File
gatheredgvcf:
type: File
outputBinding:
- glob: "*g.vcf.gz"
+ glob: "*.g.vcf.gz"
baseCommand: /gatk/gatk
- "--java-options"
- "-Xmx8G"
- GatherVcfs
- - prefix: "-I"
- valueFrom: $(inputs.gvcflist.basename)
+ - "-I"
+ - $(inputs.gvcf1.basename)
+ - "-I"
+ - $(inputs.gvcf2.basename)
- prefix: "-O"
- valueFrom: $(inputs.sample)g.vcf.gz
+ valueFrom: $(inputs.sample).g.vcf.gz