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"]
      identifier: biotools:bcftools
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"
  - - meta2:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - regions:
        type: file
        description: |
          Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited)
  - - meta3:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - targets:
        type: file
        description: |
          Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files)
  - - meta4:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - samples:
        type: file
        description: |
          Optional, file of sample names to be included or excluded.
          e.g. 'file.tsv'
  - - meta5:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - 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'
  - - meta6:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - fasta:
        type: file
        description: |
          Faidx indexed reference sequence file to determine INDEL context.
          e.g. 'reference.fa'
output:
  - stats:
      - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - "*stats.txt":
          type: file
          description: Text output file containing stats
          pattern: "*_{stats.txt}"
  - versions:
      - versions.yml:
          type: file
          description: File containing software versions
          pattern: "versions.yml"
authors:
  - "@joseespinosa"
  - "@drpatelh"
  - "@SusiJo"
  - "@TCLamnidis"
maintainers:
  - "@joseespinosa"
  - "@drpatelh"
  - "@SusiJo"
  - "@TCLamnidis"
