name: peddy
description: Manipulation, validation and exploration of pedigrees
keywords:
  - pedigrees
  - ped
  - family

tools:
  - peddy:
      description: genotype, ped correspondence check, ancestry check, sex check. directly, quickly on VCF
      homepage: https://github.com/brentp/peddy
      documentation: https://peddy.readthedocs.io/en/latest/
      tool_dev_url: https://github.com/brentp/peddy
      doi: "10.1016/j.ajhg.2017.01.017"
      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.gz}"
  - ped:
      type: file
      description: PED/FAM file
      pattern: "*.{ped,fam}"
  - vcf_tbi:
      type: file
      description: TBI file
      pattern: "*.{vcf.gz.tbi}"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - ped:
      type: file
      description: PED/FAM file
      pattern: "*.peddy.{ped}"
  - html:
      type: file
      description: HTML file
      pattern: "*.{html}"
  - csv:
      type: file
      description: CSV file
      pattern: "*.{csv}"
  - png:
      type: file
      description: PNG file
      pattern: "*.{png}"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@rannick"
