Nextflow Registry | nf-core/krakentools/extractkrakenreads@0.0.0-0c7146d

nf-core/krakentools/extractkrakenreads @ 0.0.0-0c7146d

Extract reads classified at any user-specified taxonomy IDs.

kraken2 krakentools metagenomics

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @LilyAnderssonLee

Maintainers: @LilyAnderssonLee

Extract reads classified at any user-specified taxonomy IDs.

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

include { KRAKENTOOLS_EXTRACTKRAKENREADS } from 'nf-core/krakentools/extractkrakenreads'

MIT License

Process

`Name`	`KRAKENTOOLS_EXTRACTKRAKENREADS`

Input 4 channels

`taxid` string	A list of taxid separated by spaces

#2 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`classified_reads_assignment` file	A file contains the taxonomic classification of each input read. `*.{classifiedreads.txt}`

#3 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`classified_reads_fastq` file	Classified reads as belonging to any of the taxa on the kraken2 database. `*.{fastq.gz}`

#4 tuple

`meta3` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`report` file	Optional Kraken2 report containing stats about classified and not classified reads. `*.{report.txt}`

Output 2 channels

#1 versions

`versions.yml` file	File containing software versions `versions.yml`

#2 extracted_kraken2_reads tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.{fastq.gz,fasta.gz}` file	Reads assigned to a taxid list. `*.{fastq.gz,fasta.gz}`

Tool	Description	Homepage
krakentools	KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.	https://github.com/jenniferlu717/KrakenTools

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 18:51:25 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Fkrakentools%2Fextractkrakenreads/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/krakentools/extractkrakenreads/blobs/sha256:3b7f29734a459a19a43fb52b3be28bd7b31535194eb43b7c5428e88c85810f51
Size	3.4 KB
Checksum	sha256:3b7f29734a459a19a43fb52b3be28bd7b31535194eb43b7c5428e88c85810f51
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 18:51:25 (UTC)		1	3.4 KB	-