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!
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
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.
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.
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.
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?
Christian Meesters