cwl/helper/gather-vcf.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Gathering vcf using Picard
   4 $namespaces:
   5   arv: "http://arvados.org/cwl#"
   6   cwltool: "http://commonwl.org/cwltool#"
   7
   8 requirements:
   9   DockerRequirement:
  10     dockerPull: broadinstitute/gatk:4.1.7.0
  11   ShellCommandRequirement: {}
  12   InitialWorkDirRequirement:
  13     listing:
  14       - $(inputs.gvcflist)
  15       - $(inputs.gvcf1)
  16       - $(inputs.gvcf2)
  17
  18 hints:
  19   ResourceRequirement:
  20     ramMin: 20000
  21     coresMin: 4
  22   arv:RuntimeConstraints:
  23     outputDirType: keep_output_dir
  24
  25 inputs:
  26   gvcf1:
  27     type: File
  28   gvcf2:
  29     type: File
  30   gvcflist:
  31     type: File
  32   sample: string
  33   reference:
  34     type: File
  35     secondaryFiles:
  36       - .amb
  37       - .ann
  38       - .bwt
  39       - .pac
  40       - .sa
  41       - .fai
  42       - ^.dict
  43 outputs:
  44   gatheredgvcf:
  45     type: File
  46     outputBinding:
  47       glob: "*g.vcf.gz"
  48
  49 baseCommand: /gatk/gatk
  50
  51 arguments:
  52   - "--java-options"
  53   - "-Xmx8G"
  54   - GatherVcfs
  55   - prefix: "-I"
  56     valueFrom: $(inputs.gvcflist.basename)
  57   - prefix: "-O"
  58     valueFrom: $(inputs.sample)g.vcf.gz