Annotation of bacterial genomes (isolates, MAGs) and plasmids
Input
name:type
description
pattern
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.
*.{fa,fas,fna,fasta}
db:file
Path to the Bakta database directory. Must have amrfinderplus database directory already installed within it (in a directory called ‘amrfinderplus-db/’).
proteins:file
FASTA/GenBank file of trusted proteins to first annotate from (optional)
*.{fa,fas,fna,fasta,faa}
prodigal_tf:file
Training file to use for Prodigal for CDS prediction(optional)
*.{tf,trn}
regions:file
GFF3 or GenBank file of pre-annotated regions (optional)
*.{gbff,gff3}
hmms:file
HMM database file for custom annotation (optional)
*.hmm
Output
name:type
description
pattern
embl
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.embl:file
annotations & sequences in (multi) EMBL format
*.embl
faa
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.faa:file
CDS/sORF amino acid sequences as FASTA
*.faa
ffn
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.ffn:file
feature nucleotide sequences as FASTA
*.ffn
fna
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.fna:file
replicon/contig DNA sequences as FASTA
*.fna
gbff
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.gbff:file
annotations & sequences in (multi) GenBank format
*.gbff
gff
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.gff3:file
annotations & sequences in GFF3 format
*.gff3
hypotheticals_tsv
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.hypotheticals.tsv:file
additional information on hypothetical protein CDS as simple human readable tab separated values
*.hypotheticals.tsv
hypotheticals_faa
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.hypotheticals.faa:file
hypothetical protein CDS amino acid sequences as FASTA
*.hypotheticals.faa
tsv
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.tsv:file
annotations as simple human readable tab separated values
*.tsv
txt
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
${prefix}.txt:file
genome statistics and annotation summary
*.txt
versions
versions.yml:file
File containing software versions
versions.yml
Tools
bakta
GPL v3
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids.
