cwl/gvcf2fasta/scatter-gvcf2fasta_nonrefvcf-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 with NON_REF
  10 requirements:
  11   SubworkflowFeatureRequirement: {}
  12   ScatterFeatureRequirement: {}
  13 hints:
  14   DockerRequirement:
  15     dockerPull: vcfutil
  16   arv:IntermediateOutput:
  17     outputTTL: 604800
  18
  19 inputs:
  20   sampleids:
  21     type: string[]
  22     label: Sample IDs
  23   vcfs:
  24     type: File[]
  25     label: Input VCFs
  26   gqcutoff:
  27     type: int
  28     label: GQ (Genotype Quality) cutoff for filtering
  29   genomebed:
  30     type: File
  31     label: Whole genome BED
  32   ref:
  33     type: File
  34     label: Reference FASTA
  35
  36 outputs:
  37   fas:
  38     type:
  39       type: array
  40       items:
  41         type: array
  42         items: File
  43     label: Output pairs of FASTAs
  44     outputSource: gvcf2fasta_nonrefvcf-wf/fas
  45
  46 steps:
  47   gvcf2fasta_nonrefvcf-wf:
  48     run: gvcf2fasta_nonrefvcf-wf.cwl
  49     scatter: [sampleid, vcf]
  50     scatterMethod: dotproduct
  51     in:
  52       sampleid: sampleids
  53       vcf: vcfs
  54       gqcutoff: gqcutoff
  55       genomebed: genomebed
  56       ref: ref
  57     out: [fas]