WGS-processing/cwl/helper/gatk-applyBQSR.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Applying base quality score recalibration
   4
   5 $namespaces:
   6   arv: "http://arvados.org/cwl#"
   7   cwltool: "http://commonwl.org/cwltool#"
   8
   9 requirements:
  10   DockerRequirement:
  11     dockerPull: broadinstitute/gatk:4.1.7.0
  12   InitialWorkDirRequirement:
  13     listing:
  14       - $(inputs.bam)
  15
  16 hints:
  17   arv:RuntimeConstraints:
  18     outputDirType: keep_output_dir
  19     keep_cache: 1024
  20   ResourceRequirement:
  21     ramMin: 5000
  22     coresMin: 2
  23
  24 inputs:
  25   bam:
  26     type: File
  27   reference:
  28     type: File
  29     secondaryFiles:
  30       - .amb
  31       - .ann
  32       - .bwt
  33       - .pac
  34       - .sa
  35       - .fai
  36       - ^.dict
  37   sample: string
  38   recaltable:
  39     type: File
  40
  41 outputs:
  42   recalbam:
  43     type: File
  44     outputBinding:
  45       glob: "*nodups_BQSR.bam"
  46
  47 baseCommand: /gatk/gatk
  48
  49 arguments:
  50   - "--java-options"
  51   - "-Xmx4G"
  52   - ApplyBQSR
  53   - prefix: "-R"
  54     valueFrom: $(inputs.reference)
  55   - prefix: "-I"
  56     valueFrom: $(inputs.bam.basename)
  57   - prefix: "--bqsr-recal-file"
  58     valueFrom: $(inputs.recaltable)
  59   - prefix: "-O"
  60     valueFrom: $(inputs.sample)nodups_BQSR.bam