1 # Copyright (C) The Lightning Authors. All rights reserved.
3 # SPDX-License-Identifier: AGPL-3.0
6 arv: "http://arvados.org/cwl#"
18 arv:RuntimeConstraints:
20 outputDirType: keep_output_dir
43 baseCommand: [lightning, slice-numpy]
46 - prefix: "-input-dir="
47 valueFrom: $(inputs.libdir)
49 - prefix: "-output-dir="
50 valueFrom: $(runtime.outdir)
52 - prefix: "-match-genome="
53 valueFrom: $(inputs.matchgenome)
56 valueFrom: $(inputs.regions)
59 valueFrom: $(inputs.threads)
61 - prefix: "-merge-output="
62 valueFrom: $(inputs.mergeoutput)
64 - prefix: "-expand-regions="
65 valueFrom: $(inputs.expandregions)
68 valueFrom: $(inputs.samplescsv)
71 - prefix: "-pca-components="
72 valueFrom: $(inputs.pcacomponents)
74 - "-min-coverage=0.98"
75 - "-max-pca-tiles=100000"