name: pirate
description: Pangenome toolbox for bacterial genomes
keywords:
  - gff
  - pan-genome
  - alignment
tools:
  - pirate:
      description: Pangenome analysis and threshold evaluation toolbox
      homepage: https://github.com/SionBayliss/PIRATE
      documentation: https://github.com/SionBayliss/PIRATE/wiki
      tool_dev_url: https://github.com/SionBayliss/PIRATE
      doi: "https://doi.org/10.1093/gigascience/giz119"
      licence: ['GPL v3']

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

authors:
  - "@rpetit3"