cwl/lightning/lightning-choose-samples.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: 2
  17     ramMin: 10000
  18   arv:RuntimeConstraints:
  19     keep_cache: 20000
  20     outputDirType: keep_output_dir
  21 inputs:
  22   matchgenome: string
  23   libdir: Directory
  24   phenotypesdir: Directory
  25   trainingsetsize: float
  26   randomseed: int
  27 outputs:
  28   samplescsv:
  29     type: File
  30     outputBinding:
  31       glob: "samples.csv"
  32 baseCommand: [lightning, choose-samples]
  33 arguments:
  34   - "-local=true"
  35   - prefix: "-input-dir="
  36     valueFrom: $(inputs.libdir)
  37     separate: false
  38   - prefix: "-output-dir="
  39     valueFrom: $(runtime.outdir)
  40     separate: false
  41   - prefix: "-match-genome="
  42     valueFrom: $(inputs.matchgenome)
  43     separate: false
  44   - prefix: "-case-control-file="
  45     valueFrom: $(inputs.phenotypesdir)
  46     separate: false
  47   - "-case-control-column=AD"
  48   - prefix: "-training-set-size="
  49     valueFrom: $(inputs.trainingsetsize)
  50     separate: false
  51   - prefix: "-random-seed="
  52     valueFrom: $(inputs.randomseed)
  53     separate: false