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: Fix VCF by processing chrM
18 arv:RuntimeConstraints:
26 label: Javascript code for filtering
33 secondaryFiles: [.tbi]
34 baseCommand: [rtg, vcffilter]
37 valueFrom: $(inputs.vcf)
39 valueFrom: $(inputs.vcf.basename)
40 - prefix: "--javascript"
41 valueFrom: $(inputs.filterjs)