cwl/helper/gatk-haplotypecaller.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Germline variant calling using GATK with output gvcf
   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
  41 outputs:
  42   gvcf:
  43     type: File
  44     outputBinding:
  45       glob: "*vcf.gz"
  46
  47 baseCommand: /gatk/gatk
  48
  49 arguments:
  50   - "--java-options"
  51   - "-Xmx4G"
  52   - HaplotypeCaller
  53   - prefix: "-R"
  54     valueFrom: $(inputs.reference)
  55   - prefix: "-I"
  56     valueFrom: $(inputs.bam)
  57   - prefix: "-O"
  58     valueFrom: $(runtime.outdir)/$(inputs.sample).gatk.g.vcf.gz
  59   - prefix: "-ERC"
  60     valueFrom: "GVCF"
  61   - prefix: "-GQB"
  62     valueFrom: "5"
  63   - prefix: "-GQB"
  64     valueFrom: "20"
  65   - prefix: "-GQB"
  66     valueFrom: "60"