name: "pyrodigal"
description: Pyrodigal is a Python module that provides bindings to Prodigal, a fast, reliable protein-coding gene prediction for prokaryotic genomes.
keywords:
  - sort
  - annotation
  - prediction
  - prokaryote
tools:
  - "pyrodigal":
      description: "Pyrodigal is a Python module that provides bindings to Prodigal (ORF finder for microbial sequences) using Cython."
      homepage: "https://pyrodigal.readthedocs.org/"
      documentation: "https://pyrodigal.readthedocs.org/"
      tool_dev_url: "https://github.com/althonos/pyrodigal/"
      doi: "10.21105/joss.04296"
      licence: "['GPL v3']"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - fasta:
      type: file
      description: FASTA file
      pattern: "*.{fasta.gz,fa.gz,fna.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"
  - gff:
      type: file
      description: gene annotations in gff format
      pattern: "*.{gff.gz}"
  - faa:
      type: file
      description: protein translations file
      pattern: "*.{faa.gz}"
  - fna:
      type: file
      description: nucleotide sequences file
      pattern: "*.{fna.gz}"
  - score:
      type: file
      description: all potential genes (with scores)
      pattern: "*.{score.gz}"

authors:
  - "@louperelo"
