cwl/helper/gatk-splitintervals.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Creating interval files for scattering
   4
   5 $namespaces:
   6   arv: "http://arvados.org/cwl#"
   7   cwltool: "http://commonwl.org/cwltool#"
   8
   9 requirements:
  10   DockerRequirement:
  11     dockerPull: broadinstitute/gatk:4.1.7.0
  12
  13 hints:
  14   arv:RuntimeConstraints:
  15     outputDirType: keep_output_dir
  16     keep_cache: 1024
  17   ResourceRequirement:
  18     ramMin: 5000
  19     coresMin: 2
  20
  21 inputs:
  22   reference:
  23     type: File
  24     secondaryFiles:
  25       - .amb
  26       - .ann
  27       - .bwt
  28       - .pac
  29       - .sa
  30       - .fai
  31       - ^.dict
  32   sample: string
  33   scattercount: string
  34
  35 outputs:
  36   intervalfiles:
  37     type: File[]
  38     outputBinding:
  39       glob: "intervalfiles/*.interval_list"
  40
  41 baseCommand: /gatk/gatk
  42
  43 arguments:
  44   - "--java-options"
  45   - "-Xmx4G"
  46   - SplitIntervals
  47   - prefix: "-R"
  48     valueFrom: $(inputs.reference)
  49   - prefix: "--scatter-count"
  50     valueFrom: $(inputs.scattercount)
  51   - prefix: "--subdivision-mode"
  52     valueFrom: "BALANCING_WITHOUT_INTERVAL_SUBDIVISION"
  53   - prefix: "-O"
  54     valueFrom: "intervalfiles"