cwl/gvcf2fasta/scatter-gvcf2fasta_splitvcf-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
  17 inputs:
  18   sampleids:
  19     type: string[]
  20     label: Sample IDs
  21   splitvcfdirs:
  22     type: Directory[]
  23     label: Input directory of split gVCFs
  24   gqcutoff:
  25     type: int
  26     label: GQ (Genotype Quality) cutoff for filtering
  27   genomebed:
  28     type: File
  29     label: Whole genome BED
  30   ref:
  31     type: File
  32     label: Reference FASTA
  33
  34 outputs:
  35   fas:
  36     type:
  37       type: array
  38       items:
  39         type: array
  40         items: File
  41     label: Output pairs of FASTAs
  42     outputSource: gvcf2fasta_splitvcf-wf/fas
  43
  44 steps:
  45   gvcf2fasta_splitvcf-wf:
  46     run: gvcf2fasta_splitvcf-wf.cwl
  47     scatter: [sampleid, splitvcfdir]
  48     scatterMethod: dotproduct
  49     in:
  50       sampleid: sampleids
  51       splitvcfdir: splitvcfdirs
  52       gqcutoff: gqcutoff
  53       genomebed: genomebed
  54       ref: ref
  55     out: [fas]