The #SnakemakeHackathon2026 has ended, we are still preparing our preprint release. But, our host has prepared a note on their homepage: https://go.tum.de/946236 🥳
#Snakemake #ReproducibleComputing
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#SnakemakeHackathon2026
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RE: https://fediscience.org/@snakemake/116295568336688286
This is a big step forward: The SLURM plugin for Snakemake now supports so-called job arrays. These are cluster jobs, with ~ equal resource requirements in terms of memory and compute resources.
The change in itself was big: The purpose […]
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Did you know? We started to gather cluster profiles for Snakemake users in a little repo: https://github.com/snakemake/snakemake-cluster-profiles
They should serve as a template for others.
#HPC #Snakemake #ReproducibleComputing #SnakemakeHackathon2026
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2 of 3 continuous integration workflows are working
2/3 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.
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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 !
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At the #SnakemakeHackathon2026 in Munich last week I complied Snakemake to #Wasm and made a client-side webapp for creating and sharing workflows -> snakemake.github.io/snakemake-wa....
It has support for python, R, and a 32bit linux environment all running in your browser ❤️ 🐍
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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 #FediScience association.
And now, tired, on my way back. Thanks to […]
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Today, 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.
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Reporting in from the #SnakemakeHackathon2026 - we are at the Munich Data Science Center at TUM working on various improvements to Snakemake. On a personal note, it's been some 12 years since I made my first contributions to the codebase and it's nice to stay involved with this wonderful community.
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I learn, 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 […]
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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 […]
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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, a SQLite-DB […]
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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: github.com/snakemake/snakemake-exec...
Unfortunately, I wanted to […]
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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 […]
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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 a peak of it. The list of features, bug fixes, performance improvement and […]
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Finally, some personal progress: Thanks to @fbartusch a bug of the #SLURM executor plugin for Snakemake was fixed (dealing with nested quoting). A release is upcoming.
And: I generated my first (still faulty) test #nanopub from Snakemake 🥳
#SnakemakeHackathon2026
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good luck to the hackers at #SnakemakeHackathon2026 !
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The third day of the #SnakemakeHackathon2026 at #TUM is about to end. We were very productive and I have merged over 20 pull requests that fix various bugs, clean up code, add new functionality and improvide user as well as developer experience. Thanks a lot to all the participants!
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The #SnakemakeHackathon2026 just started! Lots of interesting topics. If you are curious: #SnakemakHackathon or #SnakemakeHackathon2026 are your hashtags to follow. 😉
#reproducibleComputing #OpenScience #Datananalysis
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This cannot be:
I am trying to compile a few stats for the #Snakemake executor plugin for #SLURM on #HPC systems. Preparing for a lighting talk at the #SnakemakeHackathon2026
PyPi: 20,000 downloads last month
BioConda: > 60,000 total (aggregated over all versions)
Impressive as it might be […]
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An example (dummy) knowledge graph describing a) a Snakemake workflow b) an example data set and c) an example analysis report for this workflow
What do you see here? This is an example knowledge graph describing a #Snakemake analysis workflow. You see the workflow description, a linked data set and a linked report.
All work done to boost #HPC user support for those conducting their workflows on HPC […]
[Original post on fediscience.org]
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The #Snakemake plugin for #SLURM on #HPC clusters will support JobArrays, soon:
1057691_1 2dcf44cc-+ rule_map_reads_wild+ 32 COMPLETED 0:0
1057691_2 2dcf44cc-+ 32 RUNNING 0:0
1057691_3 2dcf44cc-+ 32 RUNNING 0:0
1057691_4 2dcf44cc-+ 32 RUNNING 0:0
1057691_5 2dcf44cc-+ 32 RUNNING 0:0
1057691_6 […]
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lines of code (LOC) development for the Snakemake Executor Plugin for SLURM over time. Displayed are the LOCs for different directories within the repository.
All in all, the last year has been eventful. Not so much new functionality, but accounting for LOTS of exceptions on various clusters.
It is time to move forward at the #SnakemakeHackathon2026 !
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Well, I did a release today:
https://fediscience.org/@snakemake/116097371050966872
And had a wonderful, productive discussion with co-developers. Looking eagerly forward to the #SnakemakeHackathon2026!
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