WGS-processing/cwl/helper/mark-duplicates.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Marking Duplicates 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
  12 hints:
  13   ResourceRequirement:
  14     ramMin: 20000
  15     coresMin: 4
  16   arv:RuntimeConstraints:
  17     outputDirType: keep_output_dir
  18
  19 inputs:
  20   bam:
  21     type: File
  22
  23 outputs:
  24   dupbam:
  25     type: File
  26     outputBinding:
  27       glob: "*.bam"
  28   dupmetrics:
  29     type: File
  30     outputBinding:
  31       glob: "*.txt"
  32
  33 baseCommand: /gatk/gatk
  34
  35 arguments:
  36   - "--java-options"
  37   - "-Xmx8G"
  38   - MarkDuplicates
  39   - prefix: "-I"
  40     valueFrom: $(inputs.bam.path)
  41   - prefix: "-O"
  42     valueFrom: marked_dups$(inputs.bam.basename)
  43   - prefix: "-M"
  44     valueFrom: "metrics.txt"