name: "haplogrep2_classify"
description: classification into haplogroups
keywords:
  - haplogroups.
tools:
  - "haplogrep2":
      description: "A tool for mtDNA haplogroup classification."
      homepage: "https://github.com/seppinho/haplogrep-cmd"
      documentation: "https://github.com/seppinho/haplogrep-cmd"
      tool_dev_url: "https://github.com/seppinho/haplogrep-cmd"

      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - inputfile:
      type: file
      description: valid options are hsd, vcf, or fasta files
      pattern: "*.{vcf,vcf.gz,fasta,hsd}"
  - format:
      type: string
      description: either "vcf", "fasta" or "hsd"

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: text file with classification information
      pattern: "*.{txt}"

authors:
  - "@lucpen"
