name: bcftools_consensus description: Compresses VCF files keywords: - variant calling - consensus - VCF tools: - consensus: description: | Create consensus sequence by applying VCF variants to a reference fasta file. homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - vcf: type: file description: VCF file pattern: "*.{vcf}" - tbi: type: file description: tabix index file pattern: "*.{tbi}" - fasta: type: file description: FASTA reference file pattern: "*.{fasta,fa}" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - fasta: type: file description: FASTA reference consensus file pattern: "*.{fasta,fa}" - version: type: file description: File containing software version pattern: "*.{version.txt}" authors: - "@joseespinosa" - "@drpatelh"