1 # Copyright (C) The Lightning Authors. All rights reserved.
3 # SPDX-License-Identifier: AGPL-3.0
6 arv: "http://arvados.org/cwl#"
7 cwltool: "http://commonwl.org/cwltool#"
10 label: Filters gVCFs by a specified quality cutoff and cleans
13 dockerPull: arvados/l7g
17 ShellCommandRequirement: {}
19 arv:RuntimeConstraints:
24 label: Input gVCF file
25 secondaryFiles: [.tbi]
28 label: Code that filters gVCFs
31 location: src/filter-gvcf
34 label: Filtering cutoff threshold
37 label: Flag for keeping GQ represented by "."
40 label: Code that cleans gVCFs
43 location: src/cleanvcf.py
47 label: Filtered and clean gVCF
50 secondaryFiles: [.tbi]
56 - $(inputs.filtergvcf)
58 valueFrom: $(inputs.keepgqdot)
69 - $(inputs.gvcf.nameroot).gz
75 - $(inputs.gvcf.nameroot).gz