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     arv:dockerCollectionPDH: 1f430e6dd9b6be0ae78d4cffde9b1fef+892
  16   ResourceRequirement:
  17     coresMin: 96
  18     ramMin: 670000
  19   arv:RuntimeConstraints:
  20     keep_cache: 6200
  21     outputDirType: keep_output_dir
  22 inputs:
  23   saveincomplete:
  24     type: string
  25   tagset:
  26     type: File
  27   fastadirs:
  28     type:
  29       - Directory
  30       - type: array
  31         items: Directory
  32 outputs:
  33   lib:
  34     type: File
  35     outputBinding:
  36       glob: "*gob.gz"
  37 baseCommand: [lightning, import]
  38 arguments:
  39   - "-local=true"
  40   - "-loglevel=info"
  41   - "-skip-ooo=true"
  42   - "-output-tiles=true"
  43   - "-batches=1"
  44   - "-batch=0"
  45   - prefix: "-save-incomplete-tiles="
  46     valueFrom: $(inputs.saveincomplete)
  47     separate: false
  48   - prefix: "-match-chromosome"
  49     valueFrom: "^(chr)?([0-9]+|X|Y|M)$"
  50   - prefix: "-output-stats"
  51     valueFrom: "stats.json"
  52   - prefix: "-tag-library"
  53     valueFrom: $(inputs.tagset)
  54   - prefix: "-o"
  55     valueFrom: "library.gob.gz"
  56   - $(inputs.fastadirs)