Nextflow Registry | nf-core/kraken2/add@0.0.0-0c7146d

nf-core/kraken2/add @ 0.0.0-0c7146d

Adds fasta files to a Kraken2 taxonomic database

metagenomics db classification build kraken2 add

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @alxndrdiaz

Maintainers: @alxndrdiaz @jfy133

Adds fasta files to a Kraken2 taxonomic database

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

include { KRAKEN2_ADD } from 'nf-core/kraken2/add'

MIT License

Process

`Name`	`KRAKEN2_ADD`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`fasta` file	fasta file that will be added to the database `*.{fa,fasta,fna,ffn}`

`taxonomy_names` file	used for associating sequences with taxonomy IDs `*.dmp`

`taxonomy_nodes` file	tree nodes using NCBI taxonomy nomenclature `*.dmp`

`accession2taxid` file	associates sequence accession IDs to taxonomy IDs `*.accession2taxid`

`seqid2taxid` file	optional premade 2 column seq2taxid map file. Must be named seq2taxid.map. If not supplied will be generated by kraken2 itself during upstream build step. `seqid2taxid.map`

Output 4 channels

#1 taxonomy_files tuple

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

#2 seqid2taxid_map tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]` `*/`
`${prefix}/seqid2taxid.map` file	File mapping sequence IDs to taxonomy IDs, either generated or premade. `seqid2taxid.map`

#3 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

#4 library_added_files tuple

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

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	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:51:16 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fkraken2%2Fadd/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/kraken2/add/blobs/sha256:d42c799c7261ae55482f42156ae77db9ed2a98a7c197d7914fa2a9c3d27fdd6b
Size	3.4 KB
Checksum	sha256:d42c799c7261ae55482f42156ae77db9ed2a98a7c197d7914fa2a9c3d27fdd6b
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:51:16 (UTC)		1	3.4 KB	-