name: "rhocall_annotate"
description: "Markup VCF file using rho-calls."
keywords:
  - roh
  - rhocall
  - runs_of_homozygosity
tools:
  - "rhocall":
      description: "Call regions of homozygosity and make tentative UPD calls."
      homepage: "https://github.com/dnil/rhocall"
      documentation: "https://github.com/dnil/rhocall"
      tool_dev_url: "https://github.com/dnil"

      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - meta2:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - vcf:
      type: file
      description: vcf file
      pattern: "*.{vcf,vcf.gz}"
  - tbi:
      type: file
      description: vcf index file
      pattern: "*.{tbi}"
  - roh:
      type: file
      description: Bcftools roh style TSV file with CHR,POS,AZ,QUAL
      pattern: "*.{roh}"
  - bed:
      type: file
      description: BED file with AZ windows.
      pattern: "*.{bed}"

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

authors:
  - "@ramprasadn"
