cwl/preprocess/gvcf/filtercleangvcf-wf.cwl

   1 # Copyright (C) The Lightning Authors. All rights reserved.
   2 #
   3 # SPDX-License-Identifier: AGPL-3.0
   4
   5 $namespaces:
   6   arv: "http://arvados.org/cwl#"
   7   cwltool: "http://commonwl.org/cwltool#"
   8 cwlVersion: v1.0
   9 class: Workflow
  10 label: Filters gVCFs by a specified quality cutoff and cleans
  11 requirements:
  12   ScatterFeatureRequirement: {}
  13 hints:
  14   arv:RuntimeConstraints:
  15     keep_cache: 4096
  16
  17 inputs:
  18   gvcfdir:
  19     type: Directory
  20     label: Input gVCF directory
  21   cutoff:
  22     type: int
  23     label: Filtering cutoff threshold
  24   keepgqdot:
  25     type: boolean?
  26     label: Flag for keeping GQ represented by "."
  27
  28 outputs:
  29   filteredcleangvcfs:
  30     type: File[]
  31     label: Filtered clean gVCFs
  32     outputSource: filtercleangvcf/filteredcleangvcf
  33
  34 steps:
  35   getfiles:
  36     run: getfiles.cwl
  37     in:
  38       gvcfdir: gvcfdir
  39     out: [gvcfs]
  40
  41   filtercleangvcf:
  42     run: filtercleangvcf.cwl
  43     scatter: gvcf
  44     in:
  45       gvcf: getfiles/gvcfs
  46       keepgqdot: keepgqdot
  47       cutoff: cutoff
  48     out: [filteredcleangvcf]