cwl/helper/not-in-use/calc-coverage.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Marking Duplicates using Picard
   4
   5 requirements:
   6   DockerRequirement:
   7     dockerPull: broadinstitute/gatk
   8
   9 hints:
  10   ResourceRequirement:
  11     ramMin: 20000
  12     coresMin: 4
  13
  14 inputs:
  15   bam:
  16     type: File
  17
  18 outputs:
  19   dupbam:
  20     type: File
  21     outputBinding:
  22       glob: "*.bam"
  23   dupmetrics:
  24     type: File
  25     outputBinding:
  26       glob: "*.txt"
  27
  28 baseCommand: /gatk/gatk
  29
  30 arguments:
  31   - "--java-options"
  32   - "-Xmx8G"
  33   - MarkDuplicates
  34   - prefix: "-I"
  35     valueFrom: $(inputs.bam.path)
  36   - prefix: "-O"
  37     valueFrom: marked_dups$(inputs.bam.basename)
  38   - prefix: "-M"
  39     valueFrom: "metrics.txt"