name: "haplocheck"
description: |
  Haplocheck detects contamination patterns in mtDNA AND WGS sequencing studies by analyzing
  the mitochondrial DNA. Haplocheck also works as a proxy tool for nDNA studies and provides
  users a graphical report to investigate the contamination further. Internally, it uses the
  Haplogrep tool, that supports rCRS and RSRS mitochondrial versions.
keywords:
  - mitochondrial
  - mtDNA
  - contamination
tools:
  - "haplocheck":
      description: "Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitochondrial content."
      homepage: "https://github.com/genepi/haplocheck"
      documentation: "https://github.com/genepi/haplocheck"
      tool_dev_url: "https://github.com/genepi/haplocheck"
      doi: 10.1101/gr.256545.119
      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}"

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: Raw report in txt format
      pattern: "*.{txt}"

  - html:
      type: file
      description: Haplocheck HTML report
      pattern: "*.{html}"

authors:
  - "@lmtani"