Nextflow Registry | nf-core/kraken2/build@0.0.0-6c4ed3a

nf-core/kraken2/build @ 0.0.0-6c4ed3a

Builds Kraken2 database

metagenomics db classification build kraken2

Latest version: 0.0.0-6c4ed3a

Total downloads: 9

Source: nf-core/modules

Authors: @alxndrdiaz

Maintainers: @alxndrdiaz @jfy133

Summary

Builds Kraken2 database

Get started

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

include { KRAKEN2_BUILD } from 'nf-core/kraken2/build'

License

MIT License

Process

`Name`	`KRAKEN2_BUILD`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`library_added_files` file	Files present in the /library/added/ directory, including FASTA files, masked FASTAs, and prelim_map files. `*`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`seqid2taxid_map` file	File mapping sequence IDs to taxonomy IDs, either generated or premade. `seqid2taxid.map`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`taxonomy_files` file	Files present in the /taxonomy/ directory, including nodes.dmp, names.dmp, and .accession2taxid files. `*`

`cleaning` boolean	activate or deactivate (true or false) cleaning of intermediate files

Output 4 channels

#1 db tuple

meta map

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

kraken2-database directory

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

IMPORTANT: this output directory will be hardcoded as 'kraken2-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.

kraken2-database/

#2 unmapped tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`kraken2-database/unmapped*.txt` file	List of unmapped sequence files, i.e. accessions that did not map to any taxonomy ID and were excluded `unmapped*.txt`

#3 db_separated tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`kraken2-database/*k2d` file	Kraken2 k2d binary database files `*.k2d`
`kraken2-database/*map` file	Kraken2 k2d binary database taxonomy to sequencing mapping file `*.map`
`kraken2-database/library/added/*` file	Kraken2 masked FASTA files used to build the database `*.fasta`
`kraken2-database/taxonomy/*` file	Kraken2 nodes.dmp, names.dmp, and .accession2taxid taxonomy files `*.{dmp,accession2taxid}`

#4 versions_kraken2 tuple

`${task.process}` string	The name of the process
`kraken2` string	The name of the tool
`kraken2 --version 2>&1 \| head -1 \| sed "s/^.Kraken version //; s/ .//"` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
kraken2	Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies.	https://ccb.jhu.edu/software/kraken2/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:27:11 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fkraken2%2Fbuild/0.0.0-6c4ed3a/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/kraken2/build/blobs/sha256:39aea4c21262d74e3f7967e567a114aafd78ceb2540d5b4c79c66d7fe034c589