1 # Copyright (C) The Lightning Authors. All rights reserved.
3 # SPDX-License-Identifier: AGPL-3.0
6 arv: "http://arvados.org/cwl#"
15 arv:dockerCollectionPDH: 1f430e6dd9b6be0ae78d4cffde9b1fef+892
19 arv:RuntimeConstraints:
21 outputDirType: keep_output_dir
37 baseCommand: [lightning, import]
42 - "-output-tiles=true"
45 - prefix: "-save-incomplete-tiles="
46 valueFrom: $(inputs.saveincomplete)
48 - prefix: "-match-chromosome"
49 valueFrom: "^(chr)?([0-9]+|X|Y|M)$"
50 - prefix: "-output-stats"
51 valueFrom: "stats.json"
52 - prefix: "-tag-library"
53 valueFrom: $(inputs.tagset)
55 valueFrom: "library.gob.gz"