name: bcftools_sort
description: Sorts VCF files
keywords:
  - sorting
  - VCF
  - variant calling
tools:
  - sort:
      description: Sort VCF files by coordinates.
      homepage: http://samtools.github.io/bcftools/bcftools.html
      documentation: http://www.htslib.org/doc/bcftools.html
      tool_dev_url: https://github.com/samtools/bcftools
      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/BCF file to be sorted
      pattern: "*.{vcf.gz,vcf,bcf}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
  - vcf:
      type: file
      description: Sorted VCF file
      pattern: "*.{vcf.gz}"

authors:
  - "@Gwennid"
