cwl/preprocess/cgivar/cgivar2vcfbed-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: v1.0
   8 class: Workflow
   9 label: Convert CGIVAR to VCF and BED region
  10 requirements:
  11   arv:RunInSingleContainer: {}
  12 hints:
  13   DockerRequirement:
  14     dockerPull: cgivar2vcfbed
  15   ResourceRequirement:
  16     ramMin: 12000
  17 inputs:
  18   cgivar:
  19     type: File
  20     label: Input CGIVAR
  21   sample:
  22     type: string
  23     label: Sample name
  24   reference:
  25     type: File
  26     label: CRR reference used for cgatools
  27   cgascript:
  28     type: File
  29     label: Script invoking cgatools
  30   fixscript:
  31     type: File
  32     label: Script to fix VCF
  33
  34 outputs:
  35   vcfgz:
  36     type: File
  37     label: Output VCF
  38     outputSource: bedtools-intersect/vcfgz
  39   bed:
  40     type: File
  41     label: BED region VCF
  42     outputSource: gvcf_regions/bed
  43
  44 steps:
  45   cgatools-mkvcf:
  46     run: cgatools-mkvcf.cwl
  47     in:
  48       cgascript: cgascript
  49       reference: reference
  50       cgivar: cgivar
  51       sample: sample
  52     out: [vcf]
  53   fix_vcf:
  54     run: fix_vcf.cwl
  55     in:
  56       fixscript: fixscript
  57       vcf: cgatools-mkvcf/vcf
  58     out: [fixedvcf]
  59   gvcf_regions:
  60     run: gvcf_regions.cwl
  61     in:
  62       vcf: fix_vcf/fixedvcf
  63     out: [bed]
  64   bedtools-intersect:
  65     run: bedtools-intersect.cwl
  66     in:
  67       vcf: fix_vcf/fixedvcf
  68       bed: gvcf_regions/bed
  69     out: [vcfgz]