DockerRequirement:
dockerPull: broadinstitute/gatk:4.1.7.0
ShellCommandRequirement: {}
- InitialWorkDirRequirement:
- listing:
- - $(inputs.gvcf1)
- - $(inputs.gvcf2)
+ InlineJavascriptRequirement: {}
hints:
ResourceRequirement:
outputDirType: keep_output_dir
inputs:
- gvcf1:
- type: File
- gvcf2:
- type: File
+ gvcfarray: File[]
sample: string
reference:
type: File
gatheredgvcf:
type: File
outputBinding:
- glob: "*g.vcf.gz"
+ glob: "*.g.vcf.gz"
baseCommand: /gatk/gatk
arguments:
- "--java-options"
- "-Xmx8G"
- - MergeVcfs
- - prefix: "-I"
- valueFrom: $(inputs.gvcf1.basename)
- - prefix: "-I"
- valueFrom: $(inputs.gvcf2.basename)
+ - GatherVcfs
+ - shellQuote: false
+ valueFrom: >
+ ${
+ var cmd "";
+ for( var i = 0; i < inputs.gvcfarray.length; i++){
+ cmd += "\s echo " + "-I" + "\s" + inputs.gvcfsarray[i]
+ }
+ return cmd;
+ }
- prefix: "-O"
- valueFrom: $(inputs.sample)g.vcf.gz
+ valueFrom: $(inputs.sample).g.vcf.gz