cwl/gvcf2fasta/gvcf2fasta_nonrefvcf-imputation-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: Impute gVCF and convert to FASTA for gVCF with NON_REF
   8 requirements:
   9   ScatterFeatureRequirement: {}
  10   SubworkflowFeatureRequirement: {}
  11 hints:
  12   DockerRequirement:
  13     dockerPull: vcfutil
  14
  15 inputs:
  16   sampleid:
  17     type: string
  18     label: Sample ID
  19   vcf:
  20     type: File
  21     label: Input gVCF
  22   gqcutoff:
  23     type: int
  24     label: GQ (Genotype Quality) cutoff for filtering
  25   genomebed:
  26     type: File
  27     label: Whole genome BED
  28   ref:
  29     type: File
  30     label: Reference FASTA
  31   haplotypes:
  32     type: int[]
  33     label: Haplotypes of sample
  34     default: [1, 2]
  35   chrs:
  36     type: string[]
  37   refsdir: Directory
  38   mapsdir: Directory
  39   panelnocallbed: File
  40
  41 outputs:
  42   fas:
  43     type: File[]
  44     label: Output pair of FASTAs
  45     outputSource: bcftools-consensus/fa
  46
  47 steps:
  48   fixvcf-get_bed_varonlyvcf:
  49     run: fixvcf-get_bed_varonlyvcf.cwl
  50     in:
  51       sampleid: sampleid
  52       vcf: vcf
  53       gqcutoff: gqcutoff
  54       genomebed: genomebed
  55     out: [nocallbed, varonlyvcf]
  56
  57   imputation-wf:
  58     run: ../imputation/imputation-wf.cwl
  59     in:
  60       sample: sampleid
  61       chrs: chrs
  62       refsdir: refsdir
  63       mapsdir: mapsdir
  64       vcf: fixvcf-get_bed_varonlyvcf/varonlyvcf
  65       nocallbed: fixvcf-get_bed_varonlyvcf/nocallbed
  66       panelnocallbed: panelnocallbed
  67     out: [phasedimputedvcf, phasedimputednocallbed]
  68
  69   bcftools-consensus:
  70     run: bcftools-consensus.cwl
  71     scatter: haplotype
  72     in:
  73       sampleid: sampleid
  74       vcf: imputation-wf/phasedimputedvcf
  75       ref: ref
  76       haplotype: haplotypes
  77       mask: imputation-wf/phasedimputednocallbed
  78     out: [fa]