cwl/gatk-haplotypecaller.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3 label: Germline variant calling using GATK with output gvcf
   4
   5 requirements:
   6   DockerRequirement:
   7     dockerPull: broadinstitute/gatk
   8   InitialWorkDirRequirement:
   9     listing:
  10       - $(inputs.bam)
  11
  12 hints:
  13   ResourceRequirement:
  14     ramMin: 20000
  15     coresMin: 4
  16
  17 inputs:
  18   bam:
  19     type: File
  20     secondaryFiles:
  21       - .bai
  22   reference:
  23     type: File
  24     secondaryFiles:
  25       - .amb
  26       - .ann
  27       - .bwt
  28       - .pac
  29       - .sa
  30       - .fai
  31       - ^.dict
  32   sample: string
  33
  34 outputs:
  35   gvcf:
  36     type: File
  37     outputBinding:
  38       glob: "*vcf.gz"
  39
  40 baseCommand: /gatk/gatk
  41
  42 arguments:
  43   - "--java-options"
  44   - "-Xmx8G"
  45   - HaplotypeCaller
  46   - prefix: "-R"
  47     valueFrom: $(inputs.reference)
  48   - prefix: "-I"
  49     valueFrom: $(inputs.bam)
  50   - prefix: "-O"
  51     valueFrom: $(runtime.outdir)/$(inputs.sample).gatk.g.vcf.gz
  52   - prefix: "-ERC"
  53     valueFrom: "GVCF"
  54   - prefix: "-GQB"
  55     valueFrom: "5"
  56   - prefix: "-GQB"
  57     valueFrom: "20"
  58   - prefix: "-GQB"
  59     valueFrom: "60"