Nextflow Registry | nf-core/bracken/build@0.0.0-e18a462

nf-core/bracken/build @ 0.0.0-e18a462

Extends a Kraken2 database to be compatible with Bracken

kraken2 bracken database build

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @jfy133

Maintainers: @jfy133

Summary

Extends a Kraken2 database to be compatible with Bracken

Get started

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

include { BRACKEN_BUILD } from 'nf-core/bracken/build'

License

MIT License

Process

`Name`	`BRACKEN_BUILD`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`k2d` file	Kraken2 k2d binary database files `*.k2d`
`map` file	Kraken2 k2d binary database taxonomy to sequencing mapping file `*.map`
`library` file	Kraken2 masked FASTA files used to build the database `*.fasta`
`taxonomy` file	Kraken2 nodes.dmp, names.dmp, and .accession2taxid taxonomy files `*.{dmp,accession2taxid}`

Output 3 channels

#1 db tuple

meta map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

bracken-database/ directory

Directory contains the database that can be used to perform taxonomic classification

IMPORTANT: this output directory will be hardcoded as 'bracken-database/' inside the module to prevent issues of containers following symlinks in symlinks.

To give a user the option to provide custom name for the database directory within a pipeline, you should customise this name using during pipeline output publication via the pipeline's publishDir or workflow output customisation options.

bracken-database/

#2 db_separated tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`bracken-database/database*` file	Bracken kmer distribution files `database*`
`bracken-database/*k2d` file	Kraken2 k2d binary database files `*.k2d`
`bracken-database/*map` file	Kraken2 k2d binary database taxonomy to sequencing mapping file `*.map`
`bracken-database/library/added/*` file	Kraken2 masked FASTA files used to build the database `*.fasta`
`bracken-database/taxonomy/*` file	Kraken2 nodes.dmp, names.dmp, and .accession2taxid taxonomy files `*.{dmp,accession2taxid}`

#3 versions_bracken tuple

`${task.process}` string	The name of the process
`bracken` string	The name of the tool
`bracken -v \| cut -f2 -d'v'` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
bracken	Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.	https://ccb.jhu.edu/software/bracken/

Version	0.0.0-e18a462
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	20 Apr 2026 15:00:07 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fbracken%2Fbuild/0.0.0-e18a462/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/bracken/build/blobs/sha256:65df8a18e80033f5b51b7f4169c6a81b6a3e6f4ade8749464189f1e7e7b8b965
Size	3.5 KB
Checksum	sha256:65df8a18e80033f5b51b7f4169c6a81b6a3e6f4ade8749464189f1e7e7b8b965
Downloads	3

Version	Date	Status	Downloads	Size
0.0.0-6c4ed3a	23 Apr 2026 15:07:53 (UTC)		3	3.5 KB
0.0.0-e18a462	20 Apr 2026 15:00:07 (UTC)