cwl/annotation/bcftools-concat.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 cwlVersion: v1.1
   8 class: CommandLineTool
   9 requirements:
  10   ShellCommandRequirement: {}
  11 hints:
  12   DockerRequirement:
  13     dockerPull: snpeff4.3t
  14   ResourceRequirement:
  15     coresMin: 2
  16     ramMin: 10000
  17   arv:RuntimeConstraints:
  18     keep_cache: 20000
  19     outputDirType: keep_output_dir
  20 inputs:
  21   sample: string
  22   vcfs:
  23     type: File[]
  24     secondaryFiles: [.tbi]
  25 outputs:
  26   vcf:
  27     type: File
  28     outputBinding:
  29       glob: "*vcf.gz"
  30     secondaryFiles: [.tbi]
  31 baseCommand: [bcftools, concat]
  32 arguments:
  33   - $(inputs.vcfs)
  34   - "-Oz"
  35   - prefix: "-o"
  36     valueFrom: $(inputs.sample)_snpeff_dbsnp_gnomad.vcf.gz
  37   - shellQuote: false
  38     valueFrom: "&&"
  39   - "tabix"
  40   - $(inputs.sample)_snpeff_dbsnp_gnomad.vcf.gz