name: bcftools_stats
description: Generates stats from VCF files
keywords:
    - variant calling
    - stats
    - VCF
tools:
    - stats:
        description: |
          Parses VCF or BCF and produces text file stats which is suitable for
          machine processing and can be plotted using plot-vcfstats.
        homepage: http://samtools.github.io/bcftools/bcftools.html
        documentation: http://www.htslib.org/doc/bcftools.html
        doi: 10.1093/bioinformatics/btp352
        licence: ['MIT']
input:
    - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - vcf:
        type: file
        description: VCF input file
        pattern: "*.{vcf}"
output:
    - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - stats:
        type: file
        description: Text output file containing stats
        pattern: "*_{stats.txt}"
    - versions:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
authors:
    - "@joseespinosa"
    - "@drpatelh"