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}"
  - tbi:
      type: file
      description: |
        The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen.
      pattern: "*.tbi"
  - regions:
      type: file
      description: |
        Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited)
  - targets:
      type: file
      description: |
        Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files)
  - samples:
      type: file
      description: |
        Optional, file of sample names to be included or excluded.
        e.g. 'file.tsv'
  - exons:
      type: file
      description: |
        Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed).
        e.g. 'exons.tsv.gz'
  - fasta:
      type: file
      description: |
        Faidx indexed reference sequence file to determine INDEL context.
        e.g. 'reference.fa'
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"
  - "@SusiJo"
  - "@TCLamnidis"
maintainers:
  - "@joseespinosa"
  - "@drpatelh"
  - "@SusiJo"
  - "@TCLamnidis"
