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
37 baseCommand: [lightning, slice-numpy]
40 - prefix: "-input-dir="
41 valueFrom: $(inputs.libdir)
43 - prefix: "-output-dir="
44 valueFrom: $(runtime.outdir)
46 - prefix: "-match-genome="
47 valueFrom: $(inputs.matchgenome)
50 valueFrom: $(inputs.regions)
55 - prefix: "-merge-output="
56 valueFrom: $(inputs.mergeoutput)
58 - prefix: "-expand-regions="
59 valueFrom: $(inputs.expandregions)
62 valueFrom: $(inputs.samplescsv)
64 - "-single-onehot=true"
65 - "-chi2-p-value=0.000001"
67 - "-case-control-only=true"