Nextflow Registry | nf-core/taxonkit/list@0.0.0-0c7146d

nf-core/taxonkit/list @ 0.0.0-0c7146d

Generate taxonomic subtrees based on taxonids

taxonomy taxids lineage

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @jcbioinformatics

Maintainers: @jcbioinformatics

Generate taxonomic subtrees based on taxonids

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

include { TAXONKIT_LIST } from 'nf-core/taxonkit/list'

MIT License

Process

`Name`	`TAXONKIT_LIST`

Input 2 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`taxid` string	Taxon id to look up (provide either this or taxidfile, not both)
`taxidfile` file	File with taxon ids to look up, each on their own line (provide either this or name, not both)

`taxdb` file	Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz

Output 2 channels

#1 tsv tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`*.tsv` file	TSV file with taxonomic subtrees `*.tsv`

#2 versions

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

Tool	Description	Homepage
taxonkit	A Cross-platform and Efficient NCBI Taxonomy Toolkit	https://bioinf.shenwei.me/taxonkit/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:18:48 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Ftaxonkit%2Flist/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/taxonkit/list/blobs/sha256:4a84d233e7e0bda3350e2729a6b63ff4ddebf069a88cd1e81af73b484206a902
Size	2.6 KB
Checksum	sha256:4a84d233e7e0bda3350e2729a6b63ff4ddebf069a88cd1e81af73b484206a902
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:18:48 (UTC)		1	2.6 KB	-