cwl/lightning/lightning-slice-numpy-onehot.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: 660000
  18   arv:RuntimeConstraints:
  19     keep_cache: 83000
  20     outputDirType: keep_output_dir
  21 inputs:
  22   matchgenome: string
  23   libdir: Directory
  24   regions: File?
  25   mergeoutput: string
  26   expandregions: int
  27   samplescsv: File
  28 outputs:
  29   outdir:
  30     type: Directory
  31     outputBinding:
  32       glob: "."
  33   npys:
  34     type: File[]
  35     outputBinding:
  36       glob: "*npy"
  37 baseCommand: [lightning, slice-numpy]
  38 arguments:
  39   - "-local=true"
  40   - prefix: "-input-dir="
  41     valueFrom: $(inputs.libdir)
  42     separate: false
  43   - prefix: "-output-dir="
  44     valueFrom: $(runtime.outdir)
  45     separate: false
  46   - prefix: "-match-genome="
  47     valueFrom: $(inputs.matchgenome)
  48     separate: false
  49   - prefix: "-regions="
  50     valueFrom: $(inputs.regions)
  51     separate: false
  52   - prefix: "-threads="
  53     valueFrom: "20"
  54     separate: false
  55   - prefix: "-merge-output="
  56     valueFrom: $(inputs.mergeoutput)
  57     separate: false
  58   - prefix: "-expand-regions="
  59     valueFrom: $(inputs.expandregions)
  60     separate: false
  61   - prefix: "-samples="
  62     valueFrom: $(inputs.samplescsv)
  63     separate: false
  64   - "-single-onehot=true"
  65   - "-chi2-p-value=0.000001"
  66   - "-min-coverage=0.9"
  67   - "-case-control-only=true"