github.com/nf-core/modules/pull/13432 @Evangelos Karatzas another

let me know how the review looks 😛

I can guarantee you, that I will ignore this 100% of the time:

While you are here (not blocking):

modules/nf-core/freyja/{demix,boot,update}/tests/main.nf.test: the tests snapshot hand-picked versions and filenames. Use snapshot(sanitizeOutput(process.out, unstableKeys: [...])), and add a content check for each unstable channel.
modules/nf-core/freyja/demix/tests/main.nf.test.snap:20: both non-stub demix tests have identical snapshots (versions only), so the no-meta/topology branch is not distinguished.
modules/nf-core/freyja/update/tests/main.nf.test:70: the stub test name has a trailing space after stub.
modules/nf-core/freyja/*/tests/main.nf.test: put a bare assert process.success before assertAll(...), as in the template.
modules/nf-core/freyja/update/main.nf:38: the stub creates usher_barcodes.csv, but a real run creates usher_barcodes.feather. The stub also always creates curated_lineages.json, which non-SARS-CoV-2 pathogens don't produce.
modules/nf-core/freyja/demix/main.nf:13, boot/main.nf:14, variants/main.nf:13: reference data (barcodes and lineage files, fasta) come in as bare path inputs. These should be tuple val(meta2), path(...).
modules/nf-core/freyja/boot/main.nf:13: val repeats maps to --nb, which has a tool default. Pass it through ext.args instead.
modules/nf-core/freyja/demix/main.nf:18, boot/main.nf:19-20, variants/main.nf:16: output names are predictable, so use "${prefix}.tsv", "${prefix}_lineages.csv" and so on instead of globs.
modules/nf-core/freyja/update/main.nf:27: quote "${db_name}".
modules/nf-core/freyja/variants/meta.yml:27,32: ontologies: []. BAM is <http://edamontology.org/format_2572> and FASTA is <http://edamontology.org/format_1929>.
modules/nf-core/freyja/boot/meta.yml:2: the description is a whole paragraph. Trim it to one short line.

too much text, not blocking, I have things to do and places to be 😄 I'd be more likely to add it, if the agent insert it as code suggestions and I just need to click "Add to batch" if I agree

These currently sit outside the diff, that's why it's just putting it in the main PR comment. Otherwise it would go line by line, and most would be code suggestions 😛