WGS-processing/cwl/helper/gatk-applyBSQR-with-interval.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Apply 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     secondaryFiles:
  28       - .bai
  29   reference:
  30     type: File
  31     secondaryFiles:
  32       - .amb
  33       - .ann
  34       - .bwt
  35       - .pac
  36       - .sa
  37       - .fai
  38       - ^.dict
  39   sample: string
  40   recaltable:
  41     type: File
  42   intervallist:
  43     type: File
  44
  45 outputs:
  46   recalbam:
  47     type: File
  48     secondaryFiles:
  49       - .bai
  50     outputBinding:
  51       glob: "*nodups_BQSR.bam"
  52
  53 baseCommand: /gatk/gatk
  54
  55 arguments:
  56   - "--java-options"
  57   - "-Xmx4G"
  58   - ApplyBQSR
  59   - prefix: "-R"
  60     valueFrom: $(inputs.reference)
  61   - prefix: "-I"
  62     valueFrom: $(inputs.bam.basename)
  63   - prefix: "--bqsr-recal-file"
  64     valueFrom: $(inputs.recaltable)
  65   - prefix: "-L"
  66     valueFrom: $(inputs.intervallist)
  67   - prefix: "-O"
  68     valueFrom: $(inputs.sample)nodups_BQSR.bam