cwl/gatk-haplotypecaller.cwl

   1 cwlVersion: v1.1
   2 class: CommandLineTool
   3
   4 requirements:
   5   DockerRequirement:
   6     dockerPull: broadinstitute/gatk
   7   InitialWorkDirRequirement:
   8     listing:
   9       - $(inputs.bam)
  10
  11 hints:
  12   ResourceRequirement:
  13     ramMin: 10000
  14     coresMin: 4
  15
  16 arguments:
  17   - java
  18   - -jar
  19   - /gatk/gatk.jar
  20   - HaplotypeCaller
  21   - -R
  22   - $(inputs.reference)
  23   - -I
  24   - $(inputs.bam)
  25   - -O
  26   - $(runtime.outdir)/$(inputs.sample).gatk.vcf
  27
  28 inputs:
  29   bam:
  30     type: File
  31     secondaryFiles:
  32       - .bai
  33   reference:
  34     type: File
  35     secondaryFiles:
  36       - .amb
  37       - .ann
  38       - .bwt
  39       - .pac
  40       - .sa
  41       - .fai
  42       - ^.dict
  43   sample: string
  44
  45 outputs:
  46   vcf:
  47     type: File
  48     outputBinding:
  49       glob: "*vcf"