name: prokka
description: Whole genome annotation of small genomes (bacterial, archeal, viral)
keywords:
  - annotation
  - fasta
  - prokka
tools:
  - prokka:
      description: Rapid annotation of prokaryotic genomes
      homepage: https://github.com/tseemann/prokka
      doi: "10.1093/bioinformatics/btu153"
      licence: ["GPL v2"]
      identifier: biotools:prokka
input:
  - - meta:
        type: map
        description: |
          Groovy Map containing sample information
          e.g. [ id:'test', single_end:false ]
    - fasta:
        type: file
        description: |
          FASTA file to be annotated. Has to contain at least a non-empty string dummy value.
        ontologies: []
  - proteins:
      type: file
      description: FASTA file of trusted proteins to first annotate from (optional)
      ontologies: []
  - prodigal_tf:
      type: file
      description: Training file to use for Prodigal (optional)
      ontologies: []
output:
  gff:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}/*.gff:
          type: file
          description: annotation in GFF3 format, containing both sequences and annotations
          pattern: "*.{gff}"
          ontologies: []
  gbk:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}/*.gbk:
          type: file
          description: annotation in GenBank format, containing both sequences and annotations
          pattern: "*.{gbk}"
          ontologies: []
  fna:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}/*.fna:
          type: file
          description: nucleotide FASTA file of the input contig sequences
          pattern: "*.{fna}"
          ontologies: []
  faa:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}/*.faa:
          type: file
          description: protein FASTA file of the translated CDS sequences
          pattern: "*.{faa}"
          ontologies: []
  ffn:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}/*.ffn:
          type: file
          description: nucleotide FASTA file of all the prediction transcripts (CDS,
            rRNA, tRNA, tmRNA, misc_RNA)
          pattern: "*.{ffn}"
          ontologies: []
  sqn:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}/*.sqn:
          type: file
          description: an ASN1 format "Sequin" file for submission to Genbank
          pattern: "*.{sqn}"
          ontologies: []
  fsa:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}/*.fsa:
          type: file
          description: nucleotide FASTA file of the input contig sequences, used by
            "tbl2asn" to create the .sqn file
          pattern: "*.{fsa}"
          ontologies: []
  tbl:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}/*.tbl:
          type: file
          description: feature Table file, used by "tbl2asn" to create the .sqn file
          pattern: "*.{tbl}"
          ontologies: []
  err:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}/*.err:
          type: file
          description: unacceptable annotations - the NCBI discrepancy report.
          pattern: "*.{err}"
          ontologies: []
  log:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}/*.log:
          type: file
          description: contains all the output that Prokka produced during its run
          pattern: "*.{log}"
          ontologies: []
  txt:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}/*.txt:
          type: file
          description: statistics relating to the annotated features found
          pattern: "*.{txt}"
          ontologies: []
  tsv:
    - - meta:
          type: map
          description: |
            Groovy Map containing sample information
            e.g. [ id:'test', single_end:false ]
      - ${prefix}/*.tsv:
          type: file
          description: tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product)
          pattern: "*.{tsv}"
          ontologies:
            - edam: http://edamontology.org/format_3475 # TSV
  versions:
    - versions.yml:
        type: file
        description: File containing software versions
        pattern: "versions.yml"
        ontologies:
          - edam: http://edamontology.org/format_3750 # YAML
authors:
  - "@rpetit3"
maintainers:
  - "@rpetit3"
