Nextflow Registry | nf-core/krakenuniq/preloadedkrakenuniq@0.0.0-c4ed7fd

nf-core/krakenuniq/preloadedkrakenuniq @ 0.0.0-c4ed7fd

Classifies metagenomic sequence data using unique k-mer counts

classify metagenomics kmers fastq db

Latest version: 0.0.0-c4ed7fd

Total downloads: 8

Source: nf-core/modules

Authors: @mjamy @Midnighter

Maintainers: @mjamy @Midnighter

Classifies metagenomic sequence data using unique k-mer counts

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

include { KRAKENUNIQ_PRELOADEDKRAKENUNIQ } from 'nf-core/krakenuniq/preloadedkrakenuniq'

MIT License

Process

`Name`	`KRAKENUNIQ_PRELOADEDKRAKENUNIQ`

Input 6 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`sequences` file	List of input files containing sequences. All of them must be either in FASTA or FASTQ format.
`prefixes` string	List of sample identifiers or filename prefixes. Must correspond in order and length to the 'sequences', or to the number of sequencing pairs.

`sequence_type` string	Format of all given sequencing files as literal string, either 'fasta' or 'fastq'. `{fasta,fastq}`

`db` directory	KrakenUniq database

`save_output_reads` boolean	Optionally, commands are added to save classified and unclassified reads as FASTQ or FASTA files depending on the input format. When the input is paired-end, the single output FASTQ contains merged reads.

`report_file` boolean	Whether to generate a report of relative abundances.

`save_output` boolean	Whether to save a file reporting the taxonomic classification of each input read.

Output 5 channels

#1 report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.krakenuniq.report.txt` file	KrakenUniq report containing statistics about classified and unclassified reads. `*.krakenuniq.report.txt`

#2 classified_reads tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.classified.${sequence_type}.gz` file	Reads classified as belonging to any of the taxa in the KrakenUniq reference database. `*.classified.{fastq,fasta}.gz`

#3 unclassified_reads tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.unclassified.${sequence_type}.gz` file	Reads not classified to any of the taxa in the KrakenUniq reference database. `*.unclassified.{fastq,fasta}.gz`

#4 versions_krakenuniq tuple

`${task.process}` string	The name of the process
`krakenuniq` string	The name of the tool
`krakenuniq --version \| sed '1!d;s/KrakenUniq version //'` eval	The expression to obtain the version of the tool

#5 classified_assignment tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.krakenuniq.classified.txt` file	KrakenUniq output file indicating the taxonomic assignment of each input read ## DOUBLE CHECK!! `*.krakenuniq.classified.txt`

Tool	Description	Homepage
krakenuniq	Metagenomics classifier with unique k-mer counting for more specific results	https://github.com/fbreitwieser/krakenuniq

Version	0.0.0-c4ed7fd
Commit ID	c4ed7fdd281d290c622c5d93fa173effc0217fdb
Release Date	27 Apr 2026 15:00:22 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fkrakenuniq%2Fpreloadedkrakenuniq/0.0.0-c4ed7fd/download
OCI Store URL	https://public.cr.seqera.io/v2/nextflow/plugin/modules/nf-core/krakenuniq/preloadedkrakenuniq/blobs/sha256:2e85d4e83af307607dd550694e0b3ea231cb15306bf880098fdd05a8a92b121b