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)