Whole genome annotation of small genomes (bacterial, archeal, viral)
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
:file
FASTA file to be annotated. Has to contain at least a non-empty string dummy value.
proteins{:bash}
FASTA file of trusted proteins to first annotate from (optional)
prodigal_tf{:bash}
Training file to use for Prodigal (optional)
gff{:bash}
${prefix}/*.gff{:bash}
annotation in GFF3 format, containing both sequences and annotations
*.{gff}
gbk{:bash}
${prefix}/*.gbk{:bash}
annotation in GenBank format, containing both sequences and annotations
*.{gbk}
fna{:bash}
${prefix}/*.fna{:bash}
nucleotide FASTA file of the input contig sequences
*.{fna}
faa{:bash}
${prefix}/*.faa{:bash}
protein FASTA file of the translated CDS sequences
*.{faa}
ffn{:bash}
${prefix}/*.ffn{:bash}
nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA)
*.{ffn}
sqn{:bash}
${prefix}/*.sqn{:bash}
an ASN1 format “Sequin” file for submission to Genbank
*.{sqn}
fsa{:bash}
${prefix}/*.fsa{:bash}
nucleotide FASTA file of the input contig sequences, used by “tbl2asn” to create the .sqn file
*.{fsa}
tbl{:bash}
${prefix}/*.tbl{:bash}
feature Table file, used by “tbl2asn” to create the .sqn file
*.{tbl}
err{:bash}
${prefix}/*.err{:bash}
unacceptable annotations - the NCBI discrepancy report.
*.{err}
log{:bash}
${prefix}/*.log{:bash}
contains all the output that Prokka produced during its run
*.{log}
txt{:bash}
${prefix}/*.txt{:bash}
statistics relating to the annotated features found
*.{txt}
tsv{:bash}
${prefix}/*.tsv{:bash}
tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product)
*.{tsv}
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Rapid annotation of prokaryotic genomes
