#reproduciblecomputing — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #reproduciblecomputing, aggregated by home.social.
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New blog post: https://blogs.fediscience.org/rupture-de-catenaire/2026/08/09/the-2nd-snakemake-hackathon/
My reflections on the latest #SnakemakeHackathon2026 . A little late, but nevertheless.
If you want to comment, please do so under the article. Only there comments will be persistent.
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New blog post: https://blogs.fediscience.org/rupture-de-catenaire/2026/08/09/the-2nd-snakemake-hackathon/
My reflections on the latest #SnakemakeHackathon2026 . A little late, but nevertheless.
If you want to comment, please do so under the article. Only there comments will be persistent.
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RE: https://fediscience.org/@biohackrxiv/116759369371023719
> Containers enhance reproducibility ...
While this is not false per se, repeating it as an undisputable fact makes it more a mantra than something worthy to discuss. Frankly, I have seen too many containers with hard-wired program options than I am willing to even discuss this without allowing for nuance.
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RE: https://fediscience.org/@biohackrxiv/116759369371023719
> Containers enhance reproducibility ...
While this is not false per se, repeating it as an undisputable fact makes it more a mantra than something worthy to discuss. Frankly, I have seen too many containers with hard-wired program options than I am willing to even discuss this without allowing for nuance.
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RE: https://fediscience.org/@snakemake/116571962095785816
This little bit "performance improvements" lowered the number of file system access events for considerably! #Snakemake triggers many such events for keeping track of metadata. Which is important, but may cause some delays due to file system overhead - particularly on parallel and/or network file systems. The feature to outsource parts of this to sqlite was implemented during the #SnakemakeHackathon2026 . I hope, I can test the improvements next Monday!
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RE: https://fediscience.org/@snakemake/116571962095785816
This little bit "performance improvements" lowered the number of file system access events for considerably! #Snakemake triggers many such events for keeping track of metadata. Which is important, but may cause some delays due to file system overhead - particularly on parallel and/or network file systems. The feature to outsource parts of this to sqlite was implemented during the #SnakemakeHackathon2026 . I hope, I can test the improvements next Monday!
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RE: https://fediscience.org/@snakemake/116523521544819091
Software provenance with #Snakemake: Using the reporter plugin for nanopublications, we can now get slightly improved nanopublications like this one: https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g (press on the little blue arrow on the right to see the full details). Automatically captured for this workflow: https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE - again expressed a nanopub declaration. 😉
It now supports to capture the "classic" software support for #Conda and Snakemake wrappers.
There is more work to do. Let's see when and if I get to it.
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RE: https://fediscience.org/@snakemake/116523521544819091
Software provenance with #Snakemake: Using the reporter plugin for nanopublications, we can now get slightly improved nanopublications like this one: https://w3id.org/np/RAmgzfta63xx0wWc_zzQVm7kwOc4tsEOA0JJJCfsiLL1g (press on the little blue arrow on the right to see the full details). Automatically captured for this workflow: https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE - again expressed a nanopub declaration. 😉
It now supports to capture the "classic" software support for #Conda and Snakemake wrappers.
There is more work to do. Let's see when and if I get to it.
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RE: https://fediscience.org/@snakemake/116443839004108636
Now, folks, this is my first release of a Snakemake reporter plugin!
I am pretty proud of it, but it would have been impossible without the input of @johanneskoester , @tkuhn and - most of all - @fbartusch !
What is it about?
Have you ever read a #bioinformatics paper and thought: "Hugh? How did they get there? This is absolutely not #reproducibleComputing , because I cannot apply it!"
The Snakemake Workflow Management System helps researchers by generating a self-contained HTML report with all bells and whistles (all software metadata, runtime stats and publication-ready figures). And yet, I felt it is time to easy writing the materials & methods section.
Declare a worfklow #nanopub using this template: https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk and get a declaration like this: https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE
Use this reporter plugin and get all metadata reference in one other nano publication: https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE
1/3
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RE: https://fediscience.org/@snakemake/116443839004108636
Now, folks, this is my first release of a Snakemake reporter plugin!
I am pretty proud of it, but it would have been impossible without the input of @johanneskoester , @tkuhn and - most of all - @fbartusch !
What is it about?
Have you ever read a #bioinformatics paper and thought: "Hugh? How did they get there? This is absolutely not #reproducibleComputing , because I cannot apply it!"
The Snakemake Workflow Management System helps researchers by generating a self-contained HTML report with all bells and whistles (all software metadata, runtime stats and publication-ready figures). And yet, I felt it is time to easy writing the materials & methods section.
Declare a worfklow #nanopub using this template: https://w3id.org/np/RAOT7z3RA0XYlHIikne8rfUUYZrtHyrzXBD1HpI_GvcRk and get a declaration like this: https://w3id.org/np/RAjHDlPDghZzc9ZvQ3uJQNJ9Jd_KAYzZt7dk5PXKgjRyE
Use this reporter plugin and get all metadata reference in one other nano publication: https://w3id.org/np/RAK9xz_ccnu0Xhs4vX2KtqCxX44mmSt6nq-ePLeewMrFE
1/3
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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 🥳
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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 🥳
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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 of a workflow system is to make use of the vast resources of an HPC cluster. Hence, jobs are submitted to run concurrently. However, for a job array, we have to "wait" for all eligible jobs to be ready. And then we submit.
To preserve concurrent execution of other jobs which are ready to be executed, a thread pool has been introduced. In itself, I do not see job arrays as such a big feature: The LSF system profited much more from arrays than the rather lean SLURM implementation does.
BUT: the new code base will ease further development to pooling many shared memory tasks (applications which support no parallel execution or are confined to one computer by "only" supporting threading). Until then, there is more work to do.
#HPC #SLURM #Snakemake #SnakemakeHackathon2026 #ReproducibleComputing #OpenScience
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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 of a workflow system is to make use of the vast resources of an HPC cluster. Hence, jobs are submitted to run concurrently. However, for a job array, we have to "wait" for all eligible jobs to be ready. And then we submit.
To preserve concurrent execution of other jobs which are ready to be executed, a thread pool has been introduced. In itself, I do not see job arrays as such a big feature: The LSF system profited much more from arrays than the rather lean SLURM implementation does.
BUT: the new code base will ease further development to pooling many shared memory tasks (applications which support no parallel execution or are confined to one computer by "only" supporting threading). Until then, there is more work to do.
#HPC #SLURM #Snakemake #SnakemakeHackathon2026 #ReproducibleComputing #OpenScience
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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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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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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 the peak of it. The list of features, bug fixes, performance improvement and additional documentation is so long — our little announcement robot cannot display it all. Even here on FediiScience with its 1500-character limit!
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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 the peak of it. The list of features, bug fixes, performance improvement and additional documentation is so long — our little announcement robot cannot display it all. Even here on FediiScience with its 1500-character limit!
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The #SnakemakeHackathon2026 just started! Lots of interesting topics. If you are curious: #SnakemakHackathon or #SnakemakeHackathon2026 are your hashtags to follow. 😉
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The #SnakemakeHackathon2026 just started! Lots of interesting topics. If you are curious: #SnakemakHackathon or #SnakemakeHackathon2026 are your hashtags to follow. 😉
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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: ✅
- another for reports: ✅ (simple datasets are already in the #nanopub verse)
- a plugin to gather software metadata and publish as a nanopub ❌ (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 ...
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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: ✅
- another for reports: ✅ (simple datasets are already in the #nanopub verse)
- a plugin to gather software metadata and publish as a nanopub ❌ (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 ...
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I want to reach out: I have this pending release for the SLURM executor (https://github.com/snakemake/snakemake-executor-plugin-slurm/pull/412 ). It implements better error feedback (in case of hardware failures and otherwise). It would need some thorough checking, and I cannot provoke too many hardware failures. Is anyone working on an older cluster? 😉
Feedback (as issues) would be appreciated. Also nice, if you tell me it is working, here.
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I want to reach out: I have this pending release for the SLURM executor (https://github.com/snakemake/snakemake-executor-plugin-slurm/pull/412 ). It implements better error feedback (in case of hardware failures and otherwise). It would need some thorough checking, and I cannot provoke too many hardware failures. Is anyone working on an older cluster? 😉
Feedback (as issues) would be appreciated. Also nice, if you tell me it is working, here.
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The last blog post I wrote was about Life Science Support on HPC clusters. Honestly? It was more of a rant. Not a good blog post.
So, someone suggested I delete it, which I did. It took me a long time to recover. Now, I have re-written this blog post. I think it is better. I weighted every phrase. It still has some rant flavour.
The upcoming articles will have more of an example character. But I still will not be able to update on a regular basis.
#Bioinformatics #HPC #ReproducibleComputing #Snakemake #Nextflow
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The last blog post I wrote was about Life Science Support on HPC clusters. Honestly? It was more of a rant. Not a good blog post.
So, someone suggested I delete it, which I did. It took me a long time to recover. Now, I have re-written this blog post. I think it is better. I weighted every phrase. It still has some rant flavour.
The upcoming articles will have more of an example character. But I still will not be able to update on a regular basis.
#Bioinformatics #HPC #ReproducibleComputing #Snakemake #Nextflow
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@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?
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@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?
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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.
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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.
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Why? Why are so many admins tinkering with their SLURM setup?
I say tinkering because there are understandable amendments and breaking changes.
A breaking change is when you require developments made on "your" cluster really, really hard to port onto another. When admins do that, they were tinkering with the SLURM source code.
😱😱😱😱😱😱😱😱😱😱😱😱😱😱
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Why? Why are so many admins tinkering with their SLURM setup?
I say tinkering because there are understandable amendments and breaking changes.
A breaking change is when you require developments made on "your" cluster really, really hard to port onto another. When admins do that, they were tinkering with the SLURM source code.
😱😱😱😱😱😱😱😱😱😱😱😱😱😱
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RE: https://fediscience.org/@snakemake/115611862667755622
Now, this is huge!
Thanks to a contribution from Cade Mirchandani (Santa Cruz, CA), whom I met at this year's #SnakemakeHackathon users can now supply a partition profile. So, instead of wrangling #SLURM partition information into a workflow profile (indicated with --workflow-profile), we can now have a global file to contain this information.
I added a time conversion function, such that the SLURM time format is obeyed, too.
There are several other development needs, before we continue in this direction (e.g. parsing SLURM partition information directly). But a task to be done is summing this up for non-users, e.g. administrators, is due too.
In any case, I think this merits a new major version.
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RE: https://fediscience.org/@snakemake/115611862667755622
Now, this is huge!
Thanks to a contribution from Cade Mirchandani (Santa Cruz, CA), whom I met at this year's #SnakemakeHackathon users can now supply a partition profile. So, instead of wrangling #SLURM partition information into a workflow profile (indicated with --workflow-profile), we can now have a global file to contain this information.
I added a time conversion function, such that the SLURM time format is obeyed, too.
There are several other development needs, before we continue in this direction (e.g. parsing SLURM partition information directly). But a task to be done is summing this up for non-users, e.g. administrators, is due too.
In any case, I think this merits a new major version.
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This took a while. After the new version of the Snakemake paper (a rolling paper on F1000) came out, the DOI now is "working" 🥳 :
https://doi.org/10.12688/f1000research.29032.3
From my point of view, it particularly describes the working with various #HPC batch systems. And: Development did not cease. If you want to follow our announcement bot for updates: @snakemake
#Snakemake #ReproducibleComputing #DataAnalysis #OpenScience #WorkflowManagement
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This took a while. After the new version of the Snakemake paper (a rolling paper on F1000) came out, the DOI now is "working" 🥳 :
https://doi.org/10.12688/f1000research.29032.3
From my point of view, it particularly describes the working with various #HPC batch systems. And: Development did not cease. If you want to follow our announcement bot for updates: @snakemake
#Snakemake #ReproducibleComputing #DataAnalysis #OpenScience #WorkflowManagement
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Just submitted a talk for FOSDEM (been invited). They asked to attach an icon-image for the talk. So I drew one. The compute racks are difficult to identify as such, but this is as far as my aquarelle skills go.
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Just submitted a talk for FOSDEM (been invited). They asked to attach an icon-image for the talk. So I drew one. The compute racks are difficult to identify as such, but this is as far as my aquarelle skills go.
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This spring, we had a wonderful time at the CERN shaping the future of the Snakemake Workflow Management System during the Snakemake Hackathon. Next spring we will meet in Munich!
If you want to take part in the Snakemake development, you can still register here: https://indico.cern.ch/e/snakemake-meeting-2026
#Snakemake #HPC #Bioinformatics #physics #dataanalysis #ReproducibleComputing #OpenScience
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This spring, we had a wonderful time at the CERN shaping the future of the Snakemake Workflow Management System during the Snakemake Hackathon. Next spring we will meet in Munich!
If you want to take part in the Snakemake development, you can still register here: https://indico.cern.ch/e/snakemake-meeting-2026
#Snakemake #HPC #Bioinformatics #physics #dataanalysis #ReproducibleComputing #OpenScience
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Where will I be in early March 2026?
In Stuttgart! At the deRSE conference. I intend to submit a couple of work items dealing with my favourite workflow management system. And the call for contributions is open: https://mastodon.social/@de_rse/115270954346336457
To give you an idea of what I have in mind, a few hashtags:
#Snakemake #nanopub #fairdatamanagement #Fair #ReproducibleComputing
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Where will I be in early March 2026?
In Stuttgart! At the deRSE conference. I intend to submit a couple of work items dealing with my favourite workflow management system. And the call for contributions is open: https://mastodon.social/@de_rse/115270954346336457
To give you an idea of what I have in mind, a few hashtags:
#Snakemake #nanopub #fairdatamanagement #Fair #ReproducibleComputing
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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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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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Hi data analyists from Mainz,
We present a survey that explores how researchers approach computational reproducibility, especially when working with HPC and cloud infrastructure. The goal is to better understand current practices, challenges, and needs around reproducible research workflows. One of our community members co-organizes this survey ( @rupdecat ).
This is the survey link:
👉 https://ec.europa.eu/eusurvey/runner/computationalReproducibility2025The survey takes approximately 10 minutes. It is anonymous and entirely voluntary. The results will be published in a research paper and also contribute to shaping best practices and training resources that support reproducible science.
The survey is open until September 30st, 2025.
Your time and input are greatly appreciated in advancing more reproducible and reliable computational research.
Boosts are welcome - if you have a local mailing list address to share with me, please send a private message.
#HPC #cloudcomputing #ReproducibleComputing #reproducibility #OpenScience
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Dear HPC users,
A while ago, I posted about a survey that explores how researchers approach computational reproducibility, especially when working with HPC and cloud infrastructure. The goal is to better understand current practices, challenges, and needs around reproducible research workflows.
We extended the deadline to the end of this month! And we already have some 260 participants! Alas, predominantly from Germany and Belgium, only.
This is the survey link:
👉 https://ec.europa.eu/eusurvey/runner/computationalReproducibility2025The survey takes approximately 10 minutes. It is anonymous and entirely voluntary. The results will be published in a research paper and also contribute to shaping best practices and training resources that support reproducible science.
The survey is open until September 30st, 2025.
Your time and input are greatly appreciated in advancing more reproducible and reliable computational research.
Boosts are welcome - if you have a local mailing list address to share with me, please send a private message.
#HPC #cloudcomputing #ReproducibleComputing #reproducibility #OpenScience
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Dear HPC users,
A while ago, I posted about a survey that explores how researchers approach computational reproducibility, especially when working with HPC and cloud infrastructure. The goal is to better understand current practices, challenges, and needs around reproducible research workflows.
We extended the deadline to the end of this month! And we already have some 260 participants! Alas, predominantly from Germany and Belgium, only.
This is the survey link:
👉 https://ec.europa.eu/eusurvey/runner/computationalReproducibility2025The survey takes approximately 10 minutes. It is anonymous and entirely voluntary. The results will be published in a research paper and also contribute to shaping best practices and training resources that support reproducible science.
The survey is open until September 30st, 2025.
Your time and input are greatly appreciated in advancing more reproducible and reliable computational research.
Boosts are welcome - if you have a local mailing list address to share with me, please send a private message.
#HPC #cloudcomputing #ReproducibleComputing #reproducibility #OpenScience
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First day at the #NESColLab comes to a conclusion (work-wise at least). I have a half-working solution .... and will keep the suspense until a first release is ready. 😉
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First day at the #NESColLab comes to a conclusion (work-wise at least). I have a half-working solution .... and will keep the suspense until a first release is ready. 😉
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@brembs we are conducting a study in the HPC world about reproducibility: https://fediscience.org/@rupdecat/114942626807831429
Are people concerned? If they want to do research with reproducibility in mind, what is keeping them from conducting an at least good-enough approach? (We all know that 100% reproducibility is impossible even if no one is actively sabotaging a particular publication or an entire field as paper mills do.)
I do not know the answers — yet. My bet, however, is on institutional "repro-washing" (that is groups and institutions which on paper and in public value reproducible research, but fail to ease working responsibly). And on people reporting plenty of obstacles in their routines, which keep them from a best effort approach.
Also, have not read the linked article (but will and comment accordingly). But here my bet would be that the number of irreproducible articles a) varies from field to field and b) might be based estimates on unreported cases.
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@brembs we are conducting a study in the HPC world about reproducibility: https://fediscience.org/@rupdecat/114942626807831429
Are people concerned? If they want to do research with reproducibility in mind, what is keeping them from conducting an at least good-enough approach? (We all know that 100% reproducibility is impossible even if no one is actively sabotaging a particular publication or an entire field as paper mills do.)
I do not know the answers — yet. My bet, however, is on institutional "repro-washing" (that is groups and institutions which on paper and in public value reproducible research, but fail to ease working responsibly). And on people reporting plenty of obstacles in their routines, which keep them from a best effort approach.
Also, have not read the linked article (but will and comment accordingly). But here my bet would be that the number of irreproducible articles a) varies from field to field and b) might be based estimates on unreported cases.
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Interested in HPC compliant data analysis workflows?
I am offering an NHR (German association for HPC resources) course for building and using Snakemake workflows on HPC clusters in Mainz, Germany! Two days: 9. & 10. December 2025 - on-site.
To find out more and perhaps enrol, visit the course page: https://indico.zdv.uni-mainz.de/event/39/
#Snakemake #HPC #ReproducibleResearch #ReproducibleComputing
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Interested in HPC compliant data analysis workflows?
I am offering an NHR (German association for HPC resources) course for building and using Snakemake workflows on HPC clusters in Mainz, Germany! Two days: 9. & 10. December 2025 - on-site.
To find out more and perhaps enrol, visit the course page: https://indico.zdv.uni-mainz.de/event/39/
#Snakemake #HPC #ReproducibleResearch #ReproducibleComputing
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My first request to the #boost mailing list in years. I hate it, when libraries "suddenly" become deprecated and at the same time stop working altogether.
All I wanted was first to have a working example for a student to work on. 🙄
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My first request to the #boost mailing list in years. I hate it, when libraries "suddenly" become deprecated and at the same time stop working altogether.
All I wanted was first to have a working example for a student to work on. 🙄
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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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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