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: 10000
  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   vcf:
  36     type: File
  37     outputBinding:
  38       glob: "*vcf"
  39
  40 arguments:
  41   - java
  42   - -jar
  43   - /gatk/gatk.jar
  44   - HaplotypeCaller
  45   - -R
  46   - $(inputs.reference)
  47   - -I
  48   - $(inputs.bam)
  49   - -O
  50   - $(runtime.outdir)/$(inputs.sample).gatk.g.vcf
  51   - -ERC
  52   - "GVCF"