Christian Meesters2/3 accomplished ✅
Now, for a release a dependency has to be released with my two fixes, which have already been merged. Then, the world will see a new #nanopub application.
A #SnakemakeHackathon2026 result.
RE: https://fediscience.org/@snakemake/116245074392817916
Hm, I thought(!) that I fixed some issues with this bot. Appears not to be the case. Moreover, the `**docs** should be bold, not ignored. 🤦
Any way, this release is yet another leftover from the #SnakemakeHackathon2026 !
Personally, the week in Munich at the #SnakemakeHackathon2026 was really neat. I met friends and acquaintances, took the time to meet an old friend of mine not working in academia any more and the wonderful @FrankSonntag from our #FediScience association.
And now, tired, on my way back. Thanks to the railway service in Germany, I enjoy some boredom and the opportunity to do something else. Even reading a disc world novel (which is not "novel" any more) does not help.
Johannes KösterToday, the #SnakemakeHackathon2026 at the TU Munich ended with the release of Snakemake 9.17! I want to thank all participants and my co-organizers! You have been incredibly dedicated and we improved a ton of things throughout the ecosystem. While 9.17 alone is already an impressive release, more releases will come in the next days and weeks, as the remaining pull requests that have been started during the hackathon are finalized. https://snakemake.github.io
I learned, that I am the first to write a reporter plugin, which is part of the #Snakemake organization.
That will change. @fbartusch is working on an #ROCrate plugin. Yours truly is working on a #nanopub plugin. Both will ease publishing workflow analysis metadata and making our computing a bit more transparent. Our motivation? Well, did you ever read a data analysis paper (e.g. from an #Bioinformatis group) recently? See?
Other things worth mentioning? My list is biased, but I liked the demo for
- a new beautiful logging interface, which might become the default at some time (incl. colour schemes which will help colour-blind colleagues).
- an improved way to plot workflow DAGs.
For both visually appealing changes, I hope very much to post some screenshot, soon.
Which new features did I like the most?
Well, there are so many, it merits a preprint for which @egonw already lend tremendous support.
Anyway, here are my favourites:
- #Snakemake tracks all #metadata during the workflow execution. This caused many(!) file access requrests. Now, we have a SQLite-DB for that purpose, thereby lifting quite some overhead.
- containerizing workflows to a Dockerfile was possible for long time. With "--containerize apptainer" there is direct support for #apptainer
- when a workflow is aborted abruptly it cannot delete its lockfile. Now running `--unlock` will not require calculating the DAG any more.
Oh, there is much, much more. But the Changelog is already linked.
As for the little executor plugin for the #SLURM batch system (for which I promised a release supporting array job support) ... Well, only a little bug fix release could be accomplished: https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v2.5.4
Unfortunately, I wanted to use the common #Snakemake logo without the letters "#HPC" and missed one entry. So our announcement bot did not work.
Anyway, a faulty file system connection kept me from debugging the new feature. Stay tuned. It is almost ready.
We were a colourful and “scientifically diverse” group of bioinformaticians,, physicists, engineers ...
It is my hope, particularly, that with the introduction of more and more features the requirements of the #ATLAS experiment of #CERN will be met and deployment of our workflows will ease computation on #HPC clusters around the world
RE: https://fediscience.org/@snakemake/116222696140712833
What a week at the #SnakemakeHackathon2026 !
What a wonderful week with wonderful people!
We were pretty productive and this #Snakemake release is just the peak of it. The list of features, bug fixes, performance improvement and additional documentation is so long — our little announcement robot cannot display it all. Even here on FediiScience with its 1500-character limit!