WGS-processing/cwl/helper/not-in-use/check-sam.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Validate Sam using Picard
   4
   5 requirements:
   6   DockerRequirement:
   7     dockerPull: broadinstitute/gatk
   8   InitialWorkDirRequirement:
   9     listing:
  10       - $(inputs.sam)
  11
  12 hints:
  13   ResourceRequirement:
  14     ramMin: 20000
  15     coresMin: 4
  16
  17 inputs:
  18   sam:
  19     type: File
  20
  21   reference:
  22     type: File
  23     secondaryFiles:
  24       - .amb
  25       - .ann
  26       - .bwt
  27       - .pac
  28       - .sa
  29       - .fai
  30       - ^.dict
  31
  32 outputs:
  33   metrics:
  34     type: File
  35     outputBinding:
  36       glob: "*.txt"
  37
  38 baseCommand: /gatk/gatk
  39
  40 arguments:
  41   - "--java-options"
  42   - "-Xmx8G"
  43   - ValidateSamFile
  44   - prefix: "-I"
  45     valueFrom: $(inputs.sam.basename)
  46   - prefix: "-M"
  47     valueFrom: "SUMMARY"
  48   - prefix: "-O"
  49     valueFrom: "metrics.txt"
  50   - prefix: "-R"
  51     valueFrom: $(inputs.reference.path)