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"