Christian Meesters2/3 accomplished â
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.
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?
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 đ„ł
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 systems (you can run Snakemake on other platforms, too).
My to-do list:
- an assertion template for workflows: â
- another for reports: â
(simple datasets are already in the #nanopub verse)
- a plugin to gather software metadata and publish as a nanopub â (half done: #SnakemakeHackathon2026 )
Kudos to @nanopub / @tkuhn and @johanneskoester - without them this pursuit would (have been) futile! And my feeling is that @fbartusch will play an important role in any further development ...
My first time ever on this list đ . While I don't like gamification, it is certainly something I couldn't miss today when cleaning tabs.
@tkuhn perhaps, I should do a few #nanopub onboarding sessions embedded with my planned #Snakemake Hackathon and the Snakemake implementation for nanopubs in a workshop (for which I still need to do some work) next year.
I'm not sure, I followed you with your remark - is this better? https://w3id.org/np/RAADhF-xHWOeATa1pKZelZ2Jwbpjxrxn8Md-yKVRxdHho
And a fitting #nanopub đ
https://w3id.org/np/RAkRpB2EgH-CFSI_I1_KJu-e1Wifnnxr5Vylk-gIDwXSs
@Dutch_Reproducibility_Network
In fact, I am a #Snakemake co-maintainer and teacher. I was not aware of WorkflowHub - and that was an omission on my part. We actually support and favour this kind of registration: https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#uploading-workflows-to-workflowhub
In my original post, I also neglected to mention the integration of WorkflowHub with #RO-Crate and in turn, the integration of RO-Crates with nanopubs. I am actively working on a better support for #nanopub and RO-Crates with @fbartusch. The question, how I teach that stands: The #HPC world (at least my bubble) is not really supportive for #ReproducibleComputing . All #OpenScience shenanigans are frowned upon. And PIs in my vicinity are still on this level: https://phdcomics.com/comics/archive.php?comicid=1531 - so, how do we educate the educators?
I share this sentiment @nanopub
https://w3id.org/np/RAiFdv4D_zW85xY3e00XaxetTe2FQSt3nYzbuONj5TJ6M
Just, I don't think replying with another #nanopub is the way to go in a discussion. Right? And then: perhaps it is a good idea for space No.27 to work on an action plan? đ
Just a minute ago, I accidentally discovered Workflowhub (https://about.workflowhub.eu/) when browsing through a few Nanopubs. I was not aware of this repository.
A first thought: "Yet another repository to register #FAIR materials? Seriously?" Then again, I am all in favour of #reproducibleComputing and want to see more of it.
On the other hand: transparency in our work is central to the #OpenScience idea. NOT cluttering a file space so that we can be transparent in our work is paramount.
Lately, we have seen #nanopub, #ROcrates, and apparently WorkflowHub, too. (This is by no means a comprehensive list.) I wonder: Are we getting too many solutions to keep up-to-date? Are we risking frightening young researchers with the high standards we are setting? We are by no means where we want to be in terms of #transparency and #reproducibility in research, or are we?
Note, that I understand how competing systems and tool sets arise. Still, my nonrhetorical questions (1 & 2) stand.
