name: "sexdeterrmine"
description: Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars.
keywords:
  - sex determination
  - genetic sex
  - relative coverage
  - ancient dna
tools:
  - "sexdeterrmine":
      description: "A python script carry out calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data."
      homepage: "https://github.com/TCLamnidis/Sex.DetERRmine"
      documentation: "https://github.com/TCLamnidis/Sex.DetERRmine/README.md"
      tool_dev_url: "https://github.com/TCLamnidis/Sex.DetERRmine"
      doi: "https://doi.org/10.1038/s41467-018-07483-5"
      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - depth:
      type: file
      description: Output from samtools depth (with header)
      pattern: "*"

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"
  - json:
      type: file
      description: JSON formatted table of relative coverages on the X and Y, with associated error bars.
      pattern: "*.json"
  - tsv:
      type: file
      description: TSV table of relative coverages on the X and Y, with associated error bars.
      pattern: "*.tsv"

authors:
  - "@TCLamnidis"