cwl/preprocess/haploidvcf/fixgt.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   cwltool: "http://commonwl.org/cwltool#"
   8 cwlVersion: v1.0
   9 class: CommandLineTool
  10 label: Fix VCF by changing haploid calls and processing chrM
  11 requirements:
  12   DockerRequirement:
  13     dockerPull: vcfutil
  14   ResourceRequirement:
  15     coresMin: 2
  16     ramMin: 8000
  17   ShellCommandRequirement: {}
  18 hints:
  19   arv:RuntimeConstraints:
  20     keep_cache: 4096
  21 inputs:
  22   vcf:
  23     type: File
  24     label: Input VCF file
  25   filterjs:
  26     type: File
  27     label: Javascript code for filtering
  28     default:
  29       class: File
  30       location: change_gt.js
  31 outputs:
  32   fixedvcf:
  33     type: File
  34     label: Fixed VCF
  35     outputBinding:
  36       glob: "*vcf.gz"
  37     secondaryFiles: [.tbi]
  38 baseCommand: zcat
  39 arguments:
  40   - $(inputs.vcf)
  41   - shellQuote: False
  42     valueFrom: "|"
  43   - "grep"
  44   - "-v"
  45   - "Locus GQX is less than 6 for hom deletion"
  46   - shellQuote: False
  47     valueFrom: "|"
  48   - "rtg"
  49   - "vcffilter"
  50   - prefix: "-i"
  51     valueFrom: "-"
  52   - prefix: "-o"
  53     valueFrom: $(inputs.vcf.basename)
  54   - prefix: "--javascript"
  55     valueFrom: $(inputs.filterjs)