cwl/imputation/bcftools-concat.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: beagle5.4
  12   ResourceRequirement:
  13     coresMin: 2
  14     ramMin: 5000
  15     tmpdirMin: 2000
  16 inputs:
  17   sample: string
  18   vcfs:
  19     type: File[]
  20     secondaryFiles: [.tbi]
  21 outputs:
  22   vcf:
  23     type: File
  24     outputBinding:
  25       glob: "*vcf.gz"
  26     secondaryFiles: [.tbi]
  27 baseCommand: [bcftools, concat]
  28 arguments:
  29   - $(inputs.vcfs)
  30   - "-Oz"
  31   - prefix: "-o"
  32     valueFrom: $(inputs.sample)_rawimputed.vcf.gz
  33   - shellQuote: false
  34     valueFrom: "&&"
  35   - "tabix"
  36   - $(inputs.sample)_rawimputed.vcf.gz