cwl/annotation/preprocess.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   trimmedvcf:
  19     type: File
  20     outputBinding:
  21       glob: "*vcf.gz"
  22 baseCommand: awk
  23 arguments:
  24   - '{if ($1 ~ /^#/ || $4 != $5) print $0}'
  25   - $(inputs.vcf)
  26   - shellQuote: False
  27     valueFrom: "|"
  28   - "bgzip"
  29   - "-c"
  30   - shellQuote: False
  31     valueFrom: ">"
  32   - $(inputs.sample).vcf.gz