cwl/lightning/lightning-import.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: 8 #96
  17     ramMin: 25000 #670000
  18   arv:RuntimeConstraints:
  19     keep_cache: 6200
  20     outputDirType: keep_output_dir
  21 inputs:
  22   saveincomplete:
  23     type: string
  24   tagset:
  25     type: File
  26   fastadirs:
  27     type:
  28       - Directory
  29       - type: array
  30         items: Directory
  31 outputs:
  32   lib:
  33     type: File
  34     outputBinding:
  35       glob: "*gob.gz"
  36 baseCommand: [lightning, import]
  37 arguments:
  38   - "-local=true"
  39   - "-loglevel=info"
  40   - "-skip-ooo=true"
  41   - "-output-tiles=true"
  42   - "-batches=1"
  43   - "-batch=0"
  44   - prefix: "-save-incomplete-tiles="
  45     valueFrom: $(inputs.saveincomplete)
  46     separate: false
  47   - prefix: "-match-chromosome"
  48     valueFrom: "^(chr)?([0-9]+|X|Y|M)$"
  49   - prefix: "-output-stats"
  50     valueFrom: "stats.json"
  51   - prefix: "-tag-library"
  52     valueFrom: $(inputs.tagset)
  53   - prefix: "-o"
  54     valueFrom: "library.gob.gz"
  55   - $(inputs.fastadirs)