cwl/helper/fix-groups.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   fixedrgbam:
  20     type: File
  21     outputBinding:
  22       glob: "*.bam"
  23
  24 baseCommand: /gatk/gatk
  25
  26 arguments:
  27   - "--java-options"
  28   - "-Xmx8G"
  29   - AddOrReplaceReadGroups
  30   - prefix: "-I"
  31     valueFrom: $(inputs.bam.path)
  32   - prefix: "-O"
  33     valueFrom: fixedrg$(inputs.bam.basename)
  34   - prefix: "-ID"
  35     valueFrom: "H0164.2"
  36   - prefix: "-LB"
  37     valueFrom: "library1"
  38   - prefix: "-PL"
  39     valueFrom: "illumina"
  40   - prefix: "-PU"
  41     valueFrom: "H0164ALXX140820.2"
  42   - prefix: "-SM"
  43     valueFrom: "sample1"