#snakemakehackathon2025 — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #snakemakehackathon2025, aggregated by home.social.
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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 (https://zenodo.org/records/17121446) and stabilizing the JSON validator (https://zenodo.org/records/17121551).
Cool!
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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: https://snakemake.github.io/snakemake-workflow-catalog/ - findability of ready-to-use workflows has greatly improved! Also, the description on how to contribute is now easy to find.
A detailed description has been published in the #researchequals collection https://www.researchequals.com/collections/hm1w-cg under https://doi.org/10.5281/zenodo.15574642
#Snakemake #ReproducibleComputing #ReproducibleResearch #OpenScience
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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 contribution from Filipe G. Viera describes a small fix to stabilize the feature. Not only will incomplete files be removed after a crash, now it is ensured that all metadata with them are deleted too, before resuming: https://zenodo.org/records/15490098
#Snakemake #SnakemakeHackathon2025 #ReproducibleComputing #OpenScience
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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 though: Without valuable input of @dryak . Without him, I would have overlooked something crucial.
And when we talk about reproducible AI, my take is that we ought to consider workflow managers, too. Something which protocols what you have done with little effort.
#SnakemakeHackathon2025 #Snakemake #ReproducibleComputing #OpenScience