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"