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   gatheredgvcf:
  35     type: File
  36     secondaryFiles:
  37       - .tbi
  38     outputSource: merge-GVCFs/gatheredgvcf
  39
  40 steps:
  41   splitintervals:
  42     run: gatk-splitintervals.cwl
  43     in:
  44       reference: reference
  45       sample: sample
  46       scattercount: scattercount
  47     out: [intervalfiles]
  48
  49   recal-haplotypecaller:
  50     run: gatk-wf-with-interval.cwl
  51     scatter: intervallist
  52     in:
  53       bam: bam
  54       reference: reference
  55       sample: sample
  56       knownsites1: knownsites1
  57       intervallist: splitintervals/intervalfiles
  58     out: [gvcf]
  59
  60   merge-GVCFs:
  61     run: gather-array-vcf.cwl
  62     in:
  63       gvcfarray: recal-haplotypecaller/gvcf
  64       sample: sample
  65       reference: reference
  66     out: [gatheredgvcf]