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'] 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. - proteins: type: file description: FASTA file of trusted proteins to first annotate from (optional) - prodigal_tf: type: file description: Training file to use for Prodigal (optional) output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - version: type: file description: File containing software version pattern: "*.{version.txt}" - gff: type: file description: annotation in GFF3 format, containing both sequences and annotations pattern: "*.{gff}" - gbk: type: file description: annotation in GenBank format, containing both sequences and annotations pattern: "*.{gbk}" - fna: type: file description: nucleotide FASTA file of the input contig sequences pattern: "*.{fna}" - faa: type: file description: protein FASTA file of the translated CDS sequences pattern: "*.{faa}" - ffn: type: file description: nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) pattern: "*.{ffn}" - sqn: type: file description: an ASN1 format "Sequin" file for submission to Genbank pattern: "*.{sqn}" - fsa: type: file description: nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file pattern: "*.{fsa}" - tbl: type: file description: feature Table file, used by "tbl2asn" to create the .sqn file pattern: "*.{tbl}" - err: type: file description: unacceptable annotations - the NCBI discrepancy report. pattern: "*.{err}" - log: type: file description: contains all the output that Prokka produced during its run pattern: "*.{log}" - txt: type: file description: statistics relating to the annotated features found pattern: "*.{txt}" - tsv: type: file description: tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product) pattern: "*.{tsv}" authors: - "@rpetit3"