WGS-processing/cwl/helper/gatk-haplotypecaller-with-interval.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
  13 hints:
  14   arv:RuntimeConstraints:
  15     outputDirType: keep_output_dir
  16     keep_cache: 1024
  17   ResourceRequirement:
  18     ramMin: 3500
  19     coresMin: 2
  20
  21 inputs:
  22   bam:
  23     type: File
  24     secondaryFiles:
  25       - .bai
  26   reference:
  27     type: File
  28     secondaryFiles:
  29       - .amb
  30       - .ann
  31       - .bwt
  32       - .pac
  33       - .sa
  34       - .fai
  35       - ^.dict
  36   intervallist:
  37     type: File
  38   sample: string
  39
  40 outputs:
  41   gvcf:
  42     type: File
  43     secondaryFiles:
  44       - .tbi
  45     outputBinding:
  46       glob: "*vcf.gz"
  47
  48 baseCommand: /gatk/gatk
  49
  50 arguments:
  51   - "--java-options"
  52   - "-Xmx4G"
  53   - HaplotypeCaller
  54   - prefix: "-R"
  55     valueFrom: $(inputs.reference)
  56   - prefix: "-I"
  57     valueFrom: $(inputs.bam)
  58   - prefix: "-L"
  59     valueFrom: $(inputs.intervallist)
  60   - prefix: "-O"
  61     valueFrom: $(runtime.outdir)/$(inputs.sample)-$(inputs.intervallist.nameroot).gatk.g.vcf.gz
  62   - prefix: "-ERC"
  63     valueFrom: "GVCF"
  64   - prefix: "-GQB"
  65     valueFrom: "5"
  66   - prefix: "-GQB"
  67     valueFrom: "20"
  68   - prefix: "-GQB"
  69     valueFrom: "60"