Many thanks to all the contributors to the release: • @Adam Talbot • @Joon Klaps • @Sara Monzon • @mashehu • @Anna Norén • @CJ Jossart • @Michael Heuer And @Maxime Garcia for helping me during the process! The major changes of this release include: • New subworkflow:

freyja

for weighted variant analysis. • Removed unused tool:

asciigenome

are no longer in the pipeline • Removed default tool:

minia

is no longer used by default. • Major template updates: nf-core/tools v2.9 → v3.4.1 for pipeline compatibility and improvements. • MultiQC improvements:

freyja

integration and clearer reporting. • A lot of module updates • New parameters:

--skip_freyja

,

--freyja_repeats

,

--freyja_db_name

,

--freyja_lineages

,

--freyja_depthcutoff

,

--additional_annotation

, and more. • A lot of software updates • Other improvements: redundancy fixes, BLAST optimization, updates to

ivar_variants_to_vcf.py

, switch to self-hosted CI runners, fixes for Conda snaps and software versions. You can see the full changelog here