cwl/imputation/get-phasedvcf.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: CommandLineTool
   7 requirements:
   8   ShellCommandRequirement: {}
   9 hints:
  10   DockerRequirement:
  11     dockerPull: vcfutil
  12   ResourceRequirement:
  13     ramMin: 5000
  14 inputs:
  15   sample: string
  16   vcf: File
  17 outputs:
  18   phasedvcf:
  19     type: File
  20     outputBinding:
  21       glob: "*.vcf.gz"
  22     secondaryFiles: [.tbi]
  23 baseCommand: zcat
  24 arguments:
  25   - $(inputs.vcf)
  26   - shellQuote: false
  27     valueFrom: "|"
  28   - "egrep"
  29   - prefix: "-v"
  30     valueFrom: '0\|0|IMP'
  31   - shellQuote: false
  32     valueFrom: "|"
  33   - "bgzip"
  34   - "-c"
  35   - shellQuote: false
  36     valueFrom: ">"
  37   - $(inputs.sample).vcf.gz
  38   - shellQuote: false
  39     valueFrom: "&&"
  40   - "tabix"
  41   - $(inputs.sample).vcf.gz