1 # Copyright (C) The Lightning Authors. All rights reserved.
3 # SPDX-License-Identifier: AGPL-3.0
7 label: Convert gVCF to FASTA
9 ScatterFeatureRequirement: {}
25 label: GQ (Genotype Quality) cutoff for filtering
28 label: Whole genome BED
31 label: Reference FASTA
34 label: Haplotypes of sample
40 label: Output pair of FASTAs
41 outputSource: bcftools-consensus/fa
45 run: get_bed_varonlyvcf.cwl
51 out: [nocallbed, varonlyvcf]
54 run: bcftools-consensus.cwl
58 vcf: get_bed_varonlyvcf/varonlyvcf
61 mask: get_bed_varonlyvcf/nocallbed