cwl/imputation/rtg-vcffilter.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 hints:
   8   DockerRequirement:
   9     dockerPull: vcfutil
  10   ResourceRequirement:
  11     ramMin: 5000
  12 inputs:
  13   sample: string
  14   vcf:
  15     type: File
  16     secondaryFiles: [.tbi]
  17   excludebed: File
  18 outputs:
  19   filteredvcf:
  20     type: File
  21     outputBinding:
  22       glob: "*.vcf.gz"
  23     secondaryFiles: [.tbi]
  24 baseCommand: [rtg, vcffilter]
  25 arguments:
  26   - prefix: "-i"
  27     valueFrom: $(inputs.vcf)
  28   - prefix: "-o"
  29     valueFrom: $(inputs.sample).vcf.gz
  30   - prefix: "--exclude-bed"
  31     valueFrom: $(inputs.excludebed)