Nextflow Registry | nf-core/bakta/bakta@0.0.0-6c4ed3a

nf-core/bakta/bakta @ 0.0.0-6c4ed3a

Annotation of bacterial genomes (isolates, MAGs) and plasmids

annotation fasta bacteria

Latest version: 0.0.0-6c4ed3a

Total downloads: 11

Source: nf-core/modules

Authors: @rpetit3 @oschwengers @jfy133

Maintainers: @rpetit3 @oschwengers @jfy133

Annotation of bacterial genomes (isolates, MAGs) and plasmids

Add the following snippet to your workflow script to include this module.

include { BAKTA_BAKTA } from 'nf-core/bakta/bakta'

MIT License

Process

`Name`	`BAKTA_BAKTA`

Input 6 channels

#1 tuple

`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 11 channels

#1 faa tuple

`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`

#2 ffn tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.ffn` file	feature nucleotide sequences as FASTA `*.ffn`

#3 fna tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.fna` file	replicon/contig DNA sequences as FASTA `*.fna`

#4 gff tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.gff3` file	annotations & sequences in GFF3 format `*.gff3`

#5 tsv tuple

`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`

#6 txt tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.txt` file	genome statistics and annotation summary `*.txt`

#7 embl tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.embl` file	annotations & sequences in (multi) EMBL format `*.embl`

#8 gbff tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`${prefix}.gbff` file	annotations & sequences in (multi) GenBank format `*.gbff`

#9 versions_bakta tuple

`bakta`
`${task.process}` string	The name of the process