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

   1 cwlVersion: v1.1
   2 class: Workflow
   3
   4 requirements:
   5   - class: SubworkflowFeatureRequirement
   6
   7 inputs:
   8   bam:
   9     type: File
  10     secondaryFiles:
  11       - .bai
  12   reference:
  13     type: File
  14     secondaryFiles:
  15       - .amb
  16       - .ann
  17       - .bwt
  18       - .pac
  19       - .sa
  20       - .fai
  21       - ^.dict
  22   sample: string
  23   knownsites1:
  24     type: File
  25     secondaryFiles:
  26       - .tbi
  27   intervallist:
  28     type: File
  29
  30 outputs:
  31   gvcf:
  32     type: File
  33     outputSource: selectvariants/filteredgvcf
  34
  35 steps:
  36   basecalibrator:
  37     run: gatk-baserecalibrator-with-interval.cwl
  38     in:
  39       bam: bam
  40       reference: reference
  41       sample: sample
  42       knownsites1: knownsites1
  43       intervallist: intervallist
  44     out: [recaltable]
  45   applyBQSR:
  46     run: gatk-applyBSQR-with-interval.cwl
  47     in:
  48       reference: reference
  49       bam: bam
  50       sample: sample
  51       intervallist: intervallist
  52       recaltable: basecalibrator/recaltable
  53     out: [recalbam]
  54   haplotypecaller:
  55     run: gatk-haplotypecaller-with-interval.cwl
  56     in:
  57       reference: reference
  58       bam: applyBQSR/recalbam
  59       sample: sample
  60       intervallist: intervallist
  61     out: [gvcf]
  62   selectvariants:
  63     run: gatk-selectvariants.cwl
  64     in:
  65       gvcf: haplotypecaller/gvcf
  66       reference: reference
  67       sample: sample
  68     out: [filteredgvcf]