name: "glimpse_chunk"
description: Defines chunks where to run imputation
keywords:
  - chunk
  - imputation
tools:
  - "glimpse":
      description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies."
      homepage: "https://odelaneau.github.io/GLIMPSE"
      documentation: "https://odelaneau.github.io/GLIMPSE/commands.html"
      tool_dev_url: "https://github.com/odelaneau/GLIMPSE"
      doi: "10.1038/s41588-020-00756-0"
      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]

  - input:
      type: file
      description: |
        Target dataset in VCF/BCF format defined at all variable positions.
        The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
      pattern: "*.{vcf,bcf}"

  - region:
      type: string
      description: |
        Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).
        For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.
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"

  - txt:
      type: file
      description: Tab delimited output txt file containing buffer and imputation regions.
      pattern: "*.{txt}"

authors:
  - "@louislenezet"