cwl/helper/scatter-gatk-wf-with-interval.cwl

   1 $namespaces:
   2   arv: "http://arvados.org/cwl#"
   3   cwltool: "http://commonwl.org/cwltool#"
   4 cwlVersion: v1.1
   5 class: Workflow
   6
   7 requirements:
   8   - class: SubworkflowFeatureRequirement
   9   - class: ScatterFeatureRequirement
  10
  11 inputs:
  12   bam:
  13     type: File
  14     secondaryFiles:
  15       - .bai
  16   reference:
  17     type: File
  18     secondaryFiles:
  19       - .amb
  20       - .ann
  21       - .bwt
  22       - .pac
  23       - .sa
  24       - .fai
  25       - ^.dict
  26   sample: string
  27   knownsites1:
  28     type: File
  29     secondaryFiles:
  30       - .tbi
  31   scattercount: string
  32
  33 outputs:
  34   gvcf:
  35     type: File[]
  36     outputSource: recal-haplotypecaller/gvcf
  37
  38 steps:
  39   splitintervals:
  40     run: gatk-splitintervals.cwl
  41     in:
  42       reference: reference
  43       sample: sample
  44       scattercount: scattercount
  45     out: [intervalfiles]
  46
  47   recal-haplotypecaller:
  48     run: gatk-wf-with-interval.cwl
  49     scatter: intervallist
  50     in:
  51       bam: bam
  52       reference: reference
  53       sample: sample
  54       knownsites1: knownsites1
  55       intervallist: splitintervals/intervalfiles
  56     out: [gvcf]