cwl/lightning/lightning-anno2vcf.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: v1.2
   8 class: CommandLineTool
   9 requirements:
  10   NetworkAccess:
  11     networkAccess: true
  12 hints:
  13   DockerRequirement:
  14     dockerPull: lightning
  15   ResourceRequirement:
  16     coresMin: 64
  17     ramMin: 500000
  18   arv:RuntimeConstraints:
  19     keep_cache: 83000
  20     outputDirType: keep_output_dir
  21 inputs:
  22   annodir: Directory
  23 outputs:
  24   vcfdir:
  25     type: Directory
  26     outputBinding:
  27       glob: "."
  28 baseCommand: [lightning, anno2vcf]
  29 arguments:
  30   - "-local=true"
  31   - prefix: "-input-dir="
  32     valueFrom: $(inputs.annodir)
  33     separate: false
  34   - prefix: "-output-dir="
  35     valueFrom: $(runtime.outdir)
  36     separate: false