v2.1.0 - Gracious Goblin - [2026-02-10]

Added

• #117 - Updated to nf-core/tools template 3.5.1 (by @jfy133)
• #143 - Documented how to resovle KrakenUniq unbound variable jellyfish issue (❤️ to @flass for suggesting, added by @jfy133)
• #140 - Added MetaCache database building support (❤️ to @ChillarAnand for suggestion, added by @alxndrdiaz and @jfy133)
• #144 - Added tutorial on how to convert an NCBI assembly_summary.txt file to input samplesheet (❤️ to @dialvarezs for improvements, by @jfy133)

Fixed

Dependencies

Tool	Old Version	New Version
nf-core	3.4.1	3.5.1
MetaCache		2.5.0

v2.0.0 - Charming Chaac - [2025-11-14]

Added

• #108 - Document workaround for building databases from single FASTA files, e.g. from NCBI RefSeq (by @pcantalupo)
• #111 - Added sourmash reference building both for genomes and proteomes (by @Midnighter).
• #117 - Updated to nf-core/tools template 3.4.1 (by @jfy133)
• #124 - Added sylph reference building (by @jfy133 and @sofstam).

Fixed

• #110 - Corrected the documented structures of the grouped output from the PREPROCESSING subworkflow
  (by @Midnighter).
• #121 - Fix Kraken2 build failing with local files due to symlink-in-symlink mounting error with containers (❤️ to @ellmagu for reporting, fix by @jfy133)
• #122 - Update DIAMOND to support more recent versions of NCBI taxonomy (by @jfy133)
• #123 - Fix a MALT build validation check incorrectly assigned to --build_krakenuniq (by @jfy133)
• #133 - Fix Kaiju compatible renamed FASTA files being always published even if --kaiju_keepintermediates false (by @jfy133)

Dependencies

Tool	Old Version	New Version
sourmash		4.9.4
sylph		0.9.0
kraken2	2.1.5	2.1.6
tar	1.34
nf-core	3.3.2	3.4.1
DIAMOND	2.1.12	2.1.16
MultiQC	1.31	1.32
Nextflow	24.04.2	25.04.2

Deprecated

• #118 - Deprecated automated building of tar.gz archives of all databases (by @jfy133)
• #126 - Remove guidance about needed double and single quotes when giving to --<tool>_build_options as actually not necessary (by @jfy133)

v1.0 - Helpful Hydra - [2025-06-19]

Added

Initial release of nf-core/createtaxdb, created with the nf-core template.

Adds database building support for the following tools:

• (Primarily) nucleotide based
  • Bracken (added by @alxndrdiaz)
  • Centrifuge (added by @jfy133)
  • ganon (added by @jfy133)
  • KMCP (added by @alxndrdiaz)
  • KrakenUniq (added by @jfy133)
  • Kraken2 (added by @alxndrdiaz)
  • MALT (added by @jfy133 and @LilyAnderssonLee)
• (Primarily) protein based
  • DIAMOND (added by @jfy133)
  • Kaiju (added by @jfy133)

Additional optimisation when running with very large number of genomes by @BioWilko.

Tool	Old Version	New Version
Bracken		3.1
Centrifuge		1.0.4.2
DIAMOND		2.1.12
find		4.6.0
ganon		2.1.0
kaiju		1.10.0
KMCP		0.9.4
Kraken2		2.1.5
KrakenUniq		1.0.4
MALT		0.6.2
pigz		2.8
seqkit		2.9.0
tar		1.34
MultiQC		1.29
p7zip		16.02

Fixed

Dependencies

Deprecated