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   threads: int
  26   mergeoutput: string
  27   expandregions: int
  28   samplescsv: File
  29 outputs:
  30   outdir:
  31     type: Directory
  32     outputBinding:
  33       glob: "."
  34   npys:
  35     type: File[]
  36     outputBinding:
  37       glob: "*npy"
  38 baseCommand: [lightning, slice-numpy]
  39 arguments:
  40   - "-local=true"
  41   - prefix: "-input-dir="
  42     valueFrom: $(inputs.libdir)
  43     separate: false
  44   - prefix: "-output-dir="
  45     valueFrom: $(runtime.outdir)
  46     separate: false
  47   - prefix: "-match-genome="
  48     valueFrom: $(inputs.matchgenome)
  49     separate: false
  50   - prefix: "-regions="
  51     valueFrom: $(inputs.regions)
  52     separate: false
  53   - prefix: "-threads="
  54     valueFrom: $(inputs.threads)
  55     separate: false
  56   - prefix: "-merge-output="
  57     valueFrom: $(inputs.mergeoutput)
  58     separate: false
  59   - prefix: "-expand-regions="
  60     valueFrom: $(inputs.expandregions)
  61     separate: false
  62   - prefix: "-samples="
  63     valueFrom: $(inputs.samplescsv)
  64     separate: false
  65   - "-single-onehot=true"
  66   - "-chi2-p-value=0.01"
  67   - "-min-coverage=0.9"