cwl/lightning/lightning-slice-numpy.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: "matrix.*.npy"
  38   chunktagoffsetcsv:
  39     type: File
  40     outputBinding:
  41       glob: "chunk-tag-offset.csv"
  42 baseCommand: [lightning, slice-numpy]
  43 arguments:
  44   - "-local=true"
  45   - prefix: "-input-dir="
  46     valueFrom: $(inputs.libdir)
  47     separate: false
  48   - prefix: "-output-dir="
  49     valueFrom: $(runtime.outdir)
  50     separate: false
  51   - prefix: "-match-genome="
  52     valueFrom: $(inputs.matchgenome)
  53     separate: false
  54   - prefix: "-regions="
  55     valueFrom: $(inputs.regions)
  56     separate: false
  57   - prefix: "-threads="
  58     valueFrom: $(inputs.threads)
  59     separate: false
  60   - prefix: "-merge-output="
  61     valueFrom: $(inputs.mergeoutput)
  62     separate: false
  63   - prefix: "-expand-regions="
  64     valueFrom: $(inputs.expandregions)
  65     separate: false
  66   - prefix: "-samples="
  67     valueFrom: $(inputs.samplescsv)
  68     separate: false