cwl/imputation/imputation-wf.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 cwlVersion: v1.1
   6 class: Workflow
   7 requirements:
   8   SubworkflowFeatureRequirement: {}
   9 inputs:
  10   sample: string
  11   chrs:
  12     type: string[]
  13   refsdir: Directory
  14   mapsdir: Directory
  15   vcf:
  16     type: File
  17     secondaryFiles: [.tbi]
  18   nocallbed: File
  19   panelnocallbed: File
  20   panelcallbed: File
  21   genomebed: File
  22
  23 outputs:
  24   phasedimputedvcf:
  25     type: File
  26     outputSource: merge-phased-imputed-wf/phasedimputedvcf
  27   phasedimputednocallbed:
  28     type: File
  29     outputSource: merge-phased-imputed-wf/phasedimputednocallbed
  30
  31 steps:
  32   rtg-vcffilter:
  33     run: rtg-vcffilter.cwl
  34     in:
  35       sample: sample
  36       vcf: vcf
  37       excludebed: nocallbed
  38     out: [filteredvcf]
  39   scatter-beagle-wf:
  40     run: scatter-beagle-wf.cwl
  41     in:
  42       sample: sample
  43       chrs: chrs
  44       refsdir: refsdir
  45       mapsdir: mapsdir
  46       vcf: rtg-vcffilter/filteredvcf
  47     out: [rawimputedvcf]
  48   merge-phased-imputed-wf:
  49     run: merge-phased-imputed-wf.cwl
  50     in:
  51       sample: sample
  52       vcf: rtg-vcffilter/filteredvcf
  53       nocallbed: nocallbed
  54       rawimputedvcf: scatter-beagle-wf/rawimputedvcf
  55       panelnocallbed: panelnocallbed
  56       panelcallbed: panelcallbed
  57       genomebed: genomebed
  58     out: [phasedimputedvcf, phasedimputednocallbed]