Remember that I have been posting about the #SnakemakeHackathon2025 ?
I never really finished that series. But now, we have two late contributions by Ward Deboutte and @johanneskoester . One describing the polishing of the multiple extension handling of #Snakemake for named inputs ( […]
The #isc25 is over and I half-recovered from the weekend, too. Time to continue my thread summing up the #SnakemakeHackathon2025 !
To me, an important contribution was from Michael Jahn from the Charpentier Lab: A complete re-design of the workflow catalogue. Have a look […]
@dryak returning from the #isc25 I will continue this thread with something applicable everywhere, not just on #HPC clusters:
Workflow runs can crash. There are a number of possible reasons. Snakemake offers a `--rerun-incomple` flag (or short `--ri`) which lets a user resume a workflow.
This […]
Today tooting from the #ISC25 - the International Supercomputing Conference. What better opportunity to brag about something I've done to facilitate using GPUs with Snakemake?
Here is my contribution, simpler job configuration for GPU jobs:
https://doi.org/10.5281/zenodo.15551797
Not alone […]
Before I continue uploading - and I do have a couple of more contributions to add to the #ResearchEquals collection - first another contribution by Johanna Elena Schmitz and Jens Zentgraf made at the #SnakemakeHackathon2025
One difficulty when dealing with a different scientific question: Do I […]
Let's take a look at another contribution of Johanna Elena Schmitz and Jens Zentgraf from the #SnakemakeHackathon2025
Snakemake users probably know that
`$ snakemake [args] --report`
will generate a self-contained HTML report. Including all plots and #metadata a researcher's heart longs for […]
One important feature implemented in the #SnakemakeHackathon2025 : Snakemake will calculate file checksums to detect changes. If a file changes, the rule producing it needs to be re-executed when a workflow it re-triggered. But what if a file is too big for reasonable checksum calculation? You […]
One important bug fix during the #SnakemakeHackathon2025 : the config replacement. Now, users can overwrite existing configurations entirely with `--replace-workflow-config`.
Details: https://zenodo.org/records/15479268
More at https://www.researchequals.com/collections/hm1w-cg/
#Snakemake […]
Did you know? During the #SnakemakeHackathon2025 we had a staggering 194 work items!
It took a while, but now we are gathering contribution reports and present them online as a ResearchEquals (fediscience.org/@ResearchEquals@akademie... collection […]
Busy year:
- Workflow programming for Data Analysis on #HPC Systems (Course in Mainz in January): ✅
- Same Course in Dresden (February) ✅
- #SnakemakeHackathon2025 at the CERN in March: ✅
- upcoming: #OpenScience Retreat (no hashtag, yet?) in April
- International Supercomputing Conference in […]
The #SnakemakeHackathon2025 just induced another collaboration for me!
It is always good to work along with like-minded people, interested in #ReproducibleComputing, #HPC and #Bioinformatics
#OpenScience
Today, the #SnakemakeHackathon2025 at @cern.bsky.social has ended with the release of Snakemake 9.0! Huge thanks to the amazing participants and all organizers! In total there were 19 new releases within the ecosystem, including hundreds of new features and bug fixes for Snakemake and its plugins!
View onto the antiproton decelerator of the CERN. The only place there, where particles are decelerated — to conduct various experiments on tiny amounts of antimatter.
Today at the #SnakemakeHackathon2025:
We did a tour around the CERN!
But, of course, work was done, too! On cvmfs support for software deployment, many core features, improved metadata reporting, more stable SLURM executor, etc. etc. etc. Soon you will read more. 😉
The third day of the #SnakemakeHackathon2025 at @cern.bsky.social is over. 11 fantastic pull requests have been merged, fixing various bugs, enabling custom logging, improving the docs, and the expressiveness of the language. snakemake.github.io
Today is the day of closed pull request for #Snakemake. The #SnakemakeHackathon2025 participants worked at full speed!
We decided to write a white-paper summarizing our achievements rather than posting individual things. Suffice to say, that also the documentation made a great leap towards […]
The second day of the #SnakemakeHackathon2025 is over. Today I have merged 11 fantastic pull requests in the in main snakemake repo alone. And we have our first #Snakemake release during the hackathon, adding integration with xonsh for scripting and helpers for extracting params from input files.
An exciting first day of the #SnakemakeHackathon2025 at @cern.bsky.social is ending now. I have already merged several pull requests and many very productive teams have formed!
Majority of all participants to the hackathon gathered for a photo at the CERN.
#SnakemakeHackathon2025 ! We started!
At the CERN for better #ReproducibleComputing and #ReproducibleResearch .
