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

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

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.

This morning, I am travelling to the #isc25 and hit a minor bug on #researchequals. Hence, no updates in the collection.

But still a few to describe without adding the latest contributions:

For instance, this one (https://zenodo.org/records/15490064) by Filipe G. Vieira: a helper function to extract checksums from files to compare with checksums Snakemake was already able to calculate. Really handy!

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 need to re-invent the wheel (read: write a Workflow from scratch?) just to address my slightly different question?

Snakemake already allowed to incorporate "alien" workflows, even #Nextflow workflows, into desired workflows. The new contribution allows for a more dynamic contribution - with very little changes.

Check it out: https://zenodo.org/records/15489694

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.

Now, why trigger this manually? If the workflow runs successfully, now we can write (or configure):

`$ snakemake [args] --report-after-run`

and Snakemake will autogenerate the same report.

For details see https://doi.org/10.5281/zenodo.15489764

#Snakemake #ReproducibleComputing
#OpenScience

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 do not what to wait forever, after all.

This contribution describes the implementation of a threshold users may set: https://doi.org/10.5281/zenodo.15489401

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/