name: prodigal
description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
keywords:
  - sort
tools:
  - prodigal:
      description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program
      homepage: https://github.com/hyattpd/Prodigal
      documentation: https://github.com/hyattpd/prodigal/wiki
      tool_dev_url: https://github.com/hyattpd/Prodigal
      doi: "10.1186/1471-2105-11-119"
      licence: ["GPL v3"]

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - genome:
      type: file
      description: fasta/fasta.gz file
  - output_format:
      type: string
      description: Output format ("gbk"/"gff"/"sqn"/"sco")

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"
  - nucleotide_fasta:
      type: file
      description: nucleotide sequences file
      pattern: "*.{fna}"
  - amino_acid_fasta:
      type: file
      description: protein translations file
      pattern: "*.{faa}"
  - all_gene_annotations:
      type: file
      description: complete starts file
      pattern: "*.{_all.txt}"
  - gene_annotations:
      type: file
      description: gene annotations in output_format given as input
      pattern: "*.{output_format}"

authors:
  - "@grst"