cwl/preprocess/simons/make-vcf-bed-wf.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 cwlVersion: v1.0
   6 class: Workflow
   7 label: Scatter to filter VCF and make BED region
   8 requirements:
   9   ScatterFeatureRequirement: {}
  10 inputs:
  11   variantsvcfdir:
  12     type: Directory
  13     label: Input variants only VCF directory
  14   fullvcfdir:
  15     type: Directory
  16     label: Input full VCF directory
  17   qualcutoff:
  18     type: int
  19     label: Filtering QUAL cutoff
  20   gqcutoff:
  21     type: int
  22     label: Filtering GQ cutoff
  23
  24 outputs:
  25   filteredvcfs:
  26     type: File[]
  27     label: Output VCFs
  28     outputSource: filter-vcf/filteredvcf
  29   beds:
  30     type: File[]
  31     label: Output BEDs
  32     outputSource: make-bed/bed
  33
  34 steps:
  35   getvariantsvcfs:
  36     run: getfiles.cwl
  37     in:
  38       dir: variantsvcfdir
  39     out: [vcfs, samples]
  40   getfullvcfs:
  41     run: getfiles.cwl
  42     in:
  43       dir: fullvcfdir
  44     out: [vcfs, samples]
  45   filter-vcf:
  46     run: filter-vcf.cwl
  47     scatter: [vcf, sample]
  48     scatterMethod: dotproduct
  49     in:
  50       vcf: getvariantsvcfs/vcfs
  51       sample: getvariantsvcfs/samples
  52       qualcutoff: qualcutoff
  53       gqcutoff: gqcutoff
  54     out: [filteredvcf]
  55   make-bed:
  56     run: make-bed.cwl
  57     scatter: [vcf, sample]
  58     scatterMethod: dotproduct
  59     in:
  60       vcf: getfullvcfs/vcfs
  61       sample: getfullvcfs/samples
  62       qualcutoff: qualcutoff
  63       gqcutoff: gqcutoff
  64     out: [bed]