cwl/gvcf2fasta/subworkflows/scatter/scatter-gvcf2fasta-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 cwlVersion: v1.1
   8 class: Workflow
   9 label: Scatter to Convert gVCF to FASTA
  10 requirements:
  11   SubworkflowFeatureRequirement: {}
  12   ScatterFeatureRequirement: {}
  13 hints:
  14   DockerRequirement:
  15     dockerPull: vcfutil
  16   arv:IntermediateOutput:
  17     outputTTL: 604800
  18
  19 inputs:
  20   vcfsdir:
  21     type: Directory
  22     label: Input directory of VCFs
  23   genomebed:
  24     type: File
  25     label: Whole genome BED
  26   ref:
  27     type: File
  28     label: Reference FASTA
  29
  30 outputs:
  31   fas:
  32     type:
  33       type: array
  34       items:
  35         type: array
  36         items: File
  37     label: Output pairs of FASTAs
  38     outputSource: gvcf2fasta-wf/fas
  39
  40 steps:
  41   getfiles:
  42     run: helpers/getfiles.cwl
  43     in:
  44       dir: vcfsdir
  45     out: [vcfs, samples]
  46   gvcf2fasta-wf:
  47     run: gvcf2fasta/gvcf2fasta-wf.cwl
  48     scatter: [sampleid, vcf]
  49     scatterMethod: dotproduct
  50     in:
  51       sampleid: getfiles/samples
  52       vcf: getfiles/vcfs
  53       genomebed: genomebed
  54       ref: ref
  55     out: [fas]