name: bcftools_query
description: Extracts fields from VCF or BCF files and outputs them in user-defined format.
keywords:
  - query
  - variant calling
  - bcftools
  - VCF
tools:
  - query:
      description: |
        Extracts fields from VCF or BCF files and outputs them in user-defined format.
      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: |
        The vcf file to be qeuried.
      pattern: "*.{vcf.gz, vcf}"
  - tbi:
      type: file
      description: |
        The tab index for the VCF file to be inspected.
      pattern: "*.tbi"
  - regions:
      type: file
      description: |
        Optionally, restrict the operation to regions listed in this file.
  - targets:
      type: file
      description: |
        Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files)
  - samples:
      type: file
      description: |
        Optional, file of sample names to be included or excluded.
        e.g. 'file.tsv'
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - txt:
      type: file
      description: BCFTools query output file
      pattern: "*.txt"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@abhi18av"
  - "@drpatelh"