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