name: "bcftools_roh"
description: A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered.
keywords:
  - roh
tools:
  - "roh":
      description: "A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered."
      homepage: https://www.htslib.org/
      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: VCF file
      pattern: "*.{vcf,.vcf.gz}"
  - af_file:
      type: file
      description: "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF."
  - af_file_tbi:
      type: file
      description: "tbi index of af_file."
  - genetic_map:
      type: file
      description: "Genetic map in the format required also by IMPUTE2."
  - regions_file:
      type: file
      description: "Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)."
  - samples_file:
      type: file
      description: "File of sample names to include or exclude if prefixed with '^'."
  - targets_file:
      type: file
      description: "Targets can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)."

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"
  - roh:
      type: file
      description: Contains site-specific and/or per-region runs of homo/autozygosity calls.
      pattern: "*.{roh}"

authors:
  - "@ramprasadn"