cwl/helper/gatk-selectvariants.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3
   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
  12 hints:
  13   arv:RuntimeConstraints:
  14     outputDirType: keep_output_dir
  15     keep_cache: 1024
  16   ResourceRequirement:
  17     ramMin: 5000
  18     coresMin: 2
  19
  20 inputs:
  21   gvcf:
  22     type: File
  23     secondaryFiles:
  24       - .tbi
  25   reference:
  26     type: File
  27     secondaryFiles:
  28       - .amb
  29       - .ann
  30       - .bwt
  31       - .pac
  32       - .sa
  33       - .fai
  34       - ^.dict
  35   sample: string
  36
  37 outputs:
  38   genotypegvcf:
  39     type: File
  40     outputBinding:
  41       glob: "*selected.g.vcf.gz"
  42
  43 baseCommand: /gatk/gatk
  44
  45 arguments:
  46   - "--java-options"
  47   - "-Xmx4G"
  48   - SelectVariants
  49   - prefix: "-R"
  50     valueFrom: $(inputs.reference)
  51   - prefix: "--remove-unused-alternates"
  52     valueFrom: "true"
  53   - prefix: "-V"
  54     valueFrom: $(inputs.gvcf)
  55   - prefix: "-O"
  56     valueFrom: $(inputs.sample)selected.g.vcf.gz