cwl/preprocess/chrmvcf/fixchrm-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 fix VCF by processing chrM
   8 requirements:
   9   ScatterFeatureRequirement: {}
  10 inputs:
  11   vcfdir:
  12     type: Directory
  13     label: Input VCF directory
  14   filterjs:
  15     type: File
  16     label: Javascript code for filtering
  17
  18 outputs:
  19   fixedvcfs:
  20     type: File[]
  21     label: Fixed VCFs
  22     outputSource: fixchrm/fixedvcf
  23
  24 steps:
  25   getfiles:
  26     run: getfiles.cwl
  27     in:
  28       dir: vcfdir
  29     out: [vcfs]
  30   fixchrm:
  31     run: fixchrm.cwl
  32     scatter: [vcf]
  33     in:
  34       vcf: getfiles/vcfs
  35       filterjs: filterjs
  36     out: [fixedvcf]