cwl/comparevcf/comparevcf-original-lightning-wf.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 cwlVersion: v1.2
   6 class: Workflow
   7 requirements:
   8   StepInputExpressionRequirement: {}
   9 inputs:
  10   sampleid: string
  11   vcf: File
  12   nocallbed: File
  13   lightningvcf: File
  14   sdf: Directory
  15   bashscript: File
  16   header: File
  17
  18 outputs:
  19   modifiedoriginalvcf:
  20     type: File
  21     outputSource: change-GT_original/modifiedvcf
  22   modifiedlightningvcf:
  23     type: File
  24     outputSource: change-GT_lightning/modifiedvcf
  25   evaldir:
  26     type: Directory
  27     outputSource: rtg-vcfeval/evaldir
  28
  29 steps:
  30   rtg-vcffilter:
  31     run: ../imputation/rtg-vcffilter.cwl
  32     in:
  33       sample: sampleid
  34       vcf: vcf
  35       excludebed: nocallbed
  36     out: [filteredvcf]
  37
  38   change-GT_original:
  39     run: change-GT.cwl
  40     in:
  41       sampleid: sampleid
  42       suffix:
  43         valueFrom: "original"
  44       vcf: rtg-vcffilter/filteredvcf
  45       header: header
  46       bashscript: bashscript
  47     out: [modifiedvcf]
  48
  49   change-GT_lightning:
  50     run: change-GT.cwl
  51     in:
  52       sampleid: sampleid
  53       suffix:
  54         valueFrom: "lightning"
  55       vcf: lightningvcf
  56       header: header
  57       bashscript: bashscript
  58     out: [modifiedvcf]
  59
  60   rtg-vcfeval:
  61     run: rtg-vcfeval.cwl
  62     in:
  63       baselinevcf: change-GT_original/modifiedvcf
  64       callsvcf: change-GT_lightning/modifiedvcf
  65       sdf: sdf
  66     out: [evaldir]