1 # Copyright (C) The Lightning Authors. All rights reserved.
3 # SPDX-License-Identifier: AGPL-3.0
7 label: Untar, concatenate, and get no call BED and variant only VCF from gVCF
9 ShellCommandRequirement: {}
25 label: GQ (Genotype Quality) cutoff for filtering
28 label: Whole genome BED
31 label: Script to untar and concatenate vcf tar ball
34 location: src/untar-concat.sh
38 label: No call BED of gVCF
43 label: Variant only VCF
45 glob: "*_varonly.vcf.gz"
46 secondaryFiles: [.tbi]
49 - $(inputs.bashscript)
54 - "/gvcf_regions/gvcf_regions.py"
56 valueFrom: $(inputs.gqcutoff)
57 - $(inputs.sampleid).vcf.gz
60 - $(inputs.sampleid).bed
66 valueFrom: $(inputs.genomebed)
68 valueFrom: $(inputs.sampleid).bed
71 - $(inputs.sampleid)_nocall.bed
76 - $(inputs.sampleid).vcf.gz
88 - $(inputs.sampleid)_varonly.vcf.gz
92 - $(inputs.sampleid)_varonly.vcf.gz
96 - $(inputs.sampleid).vcf.gz
97 - $(inputs.sampleid).bed