Another Bactopia update!

I think the plugin is completed now! I've also started the transition from pytest to nf-test (from @lukfor.bsky.social and @sebschoenherr.bsky.social). So far nf-test has been great to work with! Haha probably should have made the transition a long time ago!

Bactopia update!

Bactopia is now compatible with @nextflow.io v25 syntax and the plugin (github.com/bactopia/nf-...) is converted to the latest structure. I'm hoping to have a development build soon.

If you're interested in testing please let me know here or at github.com/bactopia/bac...

Minor Bactopia v4 update, I have a first pass at the Nextflow v25 syntax conversion.

I converted a Bactopia Tool to v25, then used @anthropic.com Claude to some help convert the remaining Bactopia Tools.

Lots of cleaning still, but progress!

See github.com/bactopia/bac... for details on v4!

At #APHL annual conference? Check out poster 212 to learn more about Bactopia and all the fun things it can do!

Side note, this is the first time all of Bactopia is depicted in a single metro map! 🎉

@bactopia.com @nextflow.io @aphl.org

Full PDF: datasets.bactopia.com/media/2025-b...

I've made a new framework for developing sequence based typing (SBT) tools.

🐪camlhmp ("camel hump") allows for an SBT schema to be defined in YAML, disentangling the SBT logic from the code, making much easier to maintain.

See poster or learn more at: rpetit3.github.io/camlhmp/late...

Thankful for the opportunity to talk at #ASMNGS about the work we're doing at the WPHL 🦬 to further improve Bactopia! (haha also🏔️!)

Per the usual, reach out if you have any questions!

Slides are available at: bactopia.github.io/latest/impac...