cwl/lightning/lightning-slice-numpy-pca.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: 1500000
  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   pcacomponents: int
  30 outputs:
  31   outdir:
  32     type: Directory
  33     outputBinding:
  34       glob: "."
  35   pcanpy:
  36     type: File
  37     outputBinding:
  38       glob: "pca.npy"
  39   pcasamplescsv:
  40     type: File
  41     outputBinding:
  42       glob: "samples.csv"
  43 baseCommand: [lightning, slice-numpy]
  44 arguments:
  45   - "-local=true"
  46   - prefix: "-input-dir="
  47     valueFrom: $(inputs.libdir)
  48     separate: false
  49   - prefix: "-output-dir="
  50     valueFrom: $(runtime.outdir)
  51     separate: false
  52   - prefix: "-match-genome="
  53     valueFrom: $(inputs.matchgenome)
  54     separate: false
  55   - prefix: "-regions="
  56     valueFrom: $(inputs.regions)
  57     separate: false
  58   - prefix: "-threads="
  59     valueFrom: $(inputs.threads)
  60     separate: false
  61   - prefix: "-merge-output="
  62     valueFrom: $(inputs.mergeoutput)
  63     separate: false
  64   - prefix: "-expand-regions="
  65     valueFrom: $(inputs.expandregions)
  66     separate: false
  67   - prefix: "-samples="
  68     valueFrom: $(inputs.samplescsv)
  69     separate: false
  70   - "-pca=true"
  71   - prefix: "-pca-components="
  72     valueFrom: $(inputs.pcacomponents)
  73     separate: false
  74   - "-min-coverage=0.98"
  75   - "-max-pca-tiles=100000"