cwl/imputation/merge-phased-imputed-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 inputs:
   8   sample: string
   9   vcf:
  10     type: File
  11     secondaryFiles: [.tbi]
  12   nocallbed: File
  13   rawimputedvcf:
  14     type: File
  15     secondaryFiles: [.tbi]
  16   panelnocallbed: File
  17   panelcallbed: File
  18   genomebed: File
  19
  20 outputs:
  21   phasedimputedvcf:
  22     type: File
  23     outputSource: rtg-vcfmerge/phasedimputedvcf
  24   phasedimputednocallbed:
  25     type: File
  26     outputSource: bedtools-intersect_phasedimputednocallbed/intersectbed
  27
  28 steps:
  29   get-phasedvcf:
  30     run: get-phasedvcf.cwl
  31     in:
  32       sample: sample
  33       vcf: rawimputedvcf
  34     out: [phasedvcf]
  35   get-imputedvcf:
  36     run: get-imputedvcf.cwl
  37     in:
  38       sample: sample
  39       vcf: rawimputedvcf
  40     out: [imputedvcf]
  41   bedtools-intersect_phasedimputednocallbed:
  42     run: bedtools-intersect.cwl
  43     in:
  44       sample: sample
  45       a: nocallbed
  46       b: panelnocallbed
  47     out: [intersectbed]
  48   bedtools-intersect_imputationbed:
  49     run: bedtools-intersect.cwl
  50     in:
  51       sample: sample
  52       a: nocallbed
  53       b: panelcallbed
  54     out: [intersectbed]
  55   rtg-vcffilter-bedtools-intersect:
  56     run: rtg-vcffilter-bedtools-intersect.cwl
  57     in:
  58       sample: sample
  59       vcf: get-imputedvcf/imputedvcf
  60       bed: bedtools-intersect_imputationbed/intersectbed
  61     out: [filteredvcf]
  62   rtg-vcfmerge:
  63     run: rtg-vcfmerge.cwl
  64     in:
  65       sample: sample
  66       vcf: vcf
  67       phasedvcf: get-phasedvcf/phasedvcf
  68       imputedvcf: rtg-vcffilter-bedtools-intersect/filteredvcf
  69     out: [phasedimputedvcf]