cwl/imputation/scatter-beagle-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 requirements:
   8   ScatterFeatureRequirement: {}
   9 inputs:
  10   sample: string
  11   chrs:
  12     type: string[]
  13   refsdir: Directory
  14   mapsdir: Directory
  15   vcf:
  16     type: File
  17     secondaryFiles: [.tbi]
  18
  19 outputs:
  20   rawimputedvcf:
  21     type: File
  22     outputSource: bcftools-concat/vcf
  23
  24 steps:
  25   match-ref-map-chr:
  26     run: match-ref-map-chr.cwl
  27     in:
  28       chrs: chrs
  29       refsdir: refsdir
  30       mapsdir: mapsdir
  31     out: [refs, maps]
  32   beagle:
  33     scatter: [chr, ref, map]
  34     scatterMethod: dotproduct
  35     run: beagle.cwl
  36     in:
  37       sample: sample
  38       chr: chrs
  39       ref: match-ref-map-chr/refs
  40       map: match-ref-map-chr/maps
  41       vcf: vcf
  42     out: [rawimputedvcf]
  43   bcftools-concat:
  44     run: bcftools-concat.cwl
  45     in:
  46       sample: sample
  47       vcfs: beagle/rawimputedvcf
  48     out: [vcf]