name: "panaroo_run"
description: A fast and scalable tool for bacterial pangenome analysis
keywords:
  - gff
  - pan-genome
  - alignment
tools:
  - "panaroo":
      description: "panaroo - an updated pipeline for pangenome investigation"
      homepage: "https://gtonkinhill.github.io/panaroo/#/"
      documentation: "https://gtonkinhill.github.io/panaroo/#/gettingstarted/quickstart"
      tool_dev_url: "https://github.com/gtonkinhill/panaroo"
      doi: "10.1186/s13059-020-02090-4"
      licence: "['MIT']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - gff:
      type: file
      description: A set of GFF3 formatted files
      pattern: "*.{gff}"

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"
  - results:
      type: directory
      description: Directory containing Panaroo result files
      pattern: "*/*"
  - aln:
      type: file
      description: Core-genome alignment produced by Panaroo (Optional)
      pattern: "*.{fasta}"

authors:
  - "@rpetit3"
