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
38 baseCommand: [lightning, slice-numpy]
41 - prefix: "-input-dir="
42 valueFrom: $(inputs.libdir)
44 - prefix: "-output-dir="
45 valueFrom: $(runtime.outdir)
47 - prefix: "-match-genome="
48 valueFrom: $(inputs.matchgenome)
51 valueFrom: $(inputs.regions)
54 valueFrom: $(inputs.threads)
56 - prefix: "-merge-output="
57 valueFrom: $(inputs.mergeoutput)
59 - prefix: "-expand-regions="
60 valueFrom: $(inputs.expandregions)
63 valueFrom: $(inputs.samplescsv)
65 - "-single-onehot=true"
66 - "-chi2-p-value=0.01"