cwl/gvcf2fasta/gvcf2fasta_splitvcftar-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 label: Convert gVCF to FASTA for gVCF tar split by chromosome
   8 requirements:
   9   ScatterFeatureRequirement: {}
  10 hints:
  11   DockerRequirement:
  12     dockerPull: vcfutil
  13   ResourceRequirement:
  14     ramMin: 5000
  15
  16 inputs:
  17   sampleid:
  18     type: string
  19     label: Sample ID
  20   vcftar:
  21     type: File
  22     label: Input gVCF tar
  23   gqcutoff:
  24     type: int
  25     label: GQ (Genotype Quality) cutoff for filtering
  26   genomebed:
  27     type: File
  28     label: Whole genome BED
  29   ref:
  30     type: File
  31     label: Reference FASTA
  32   haplotypes:
  33     type: int[]
  34     label: Haplotypes of sample
  35     default: [1, 2]
  36
  37 outputs:
  38   fas:
  39     type: File[]
  40     label: Output pair of FASTAs
  41     outputSource: bcftools-consensus/fa
  42
  43 steps:
  44   untar-concat-get_bed_varonlyvcf:
  45     run: untar-concat-get_bed_varonlyvcf.cwl
  46     in:
  47       sampleid: sampleid
  48       vcftar: vcftar
  49       gqcutoff: gqcutoff
  50       genomebed: genomebed
  51     out: [nocallbed, varonlyvcf]
  52
  53   bcftools-consensus:
  54     run: bcftools-consensus.cwl
  55     scatter: haplotype
  56     in:
  57       sampleid: sampleid
  58       vcf: untar-concat-get_bed_varonlyvcf/varonlyvcf
  59       ref: ref
  60       haplotype: haplotypes
  61       mask: untar-concat-get_bed_varonlyvcf/nocallbed
  62     out: [fa]