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!
March 10, 2025 at 4:52 PM
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!
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!
March 14, 2025 at 10:11 PM
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!
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
Snakemake
snakemake.github.io
March 12, 2025 at 9:20 PM
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
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.
March 11, 2025 at 8:10 PM
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.
#snakemakehackathon2025 ! We started!
At the CERN for better #reproduciblecomputing and #ReproducibleResearch .
At the CERN for better #reproduciblecomputing and #ReproducibleResearch .
March 10, 2025 at 3:53 PM
#snakemakehackathon2025 ! We started!
At the CERN for better #reproduciblecomputing and #ReproducibleResearch .
At the CERN for better #reproduciblecomputing and #ReproducibleResearch .
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
It is always good to work along with like-minded people, interested in #reproduciblecomputing, #hpc and #bioinformatics
#OpenScience
March 27, 2025 at 6:15 PM
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
It is always good to work along with like-minded people, interested in #reproduciblecomputing, #hpc and #bioinformatics
#OpenScience
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 […]
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 […]
Original post on fediscience.org
fediscience.org
March 12, 2025 at 5:05 PM
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 […]
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 […]
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 ( […]
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 ( […]
Original post on fediscience.org
fediscience.org
September 16, 2025 at 12:40 PM
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 ( […]
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 […]
To me, an important contribution was from Michael Jahn from the Charpentier Lab: A complete re-design of the workflow catalogue. Have a look […]
Original post on fediscience.org
fediscience.org
June 16, 2025 at 8:30 AM
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 […]
To me, an important contribution was from Michael Jahn from the Charpentier Lab: A complete re-design of the workflow catalogue. Have a look […]
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 […]
One difficulty when dealing with a different scientific question: Do I […]
Original post on fediscience.org
fediscience.org
June 9, 2025 at 7:52 AM
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 […]
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 […]
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 […]
Original post on fediscience.org
fediscience.org
June 6, 2025 at 6:10 AM
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 […]
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 […]
Original post on fediscience.org
fediscience.org
June 5, 2025 at 10:56 AM
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 […]
Details: https://zenodo.org/records/15479268
More at https://www.researchequals.com/collections/hm1w-cg/
#snakemake […]
Original post on fediscience.org
fediscience.org
June 4, 2025 at 7:15 AM
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 […]
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 (https://fediscience.org/@ResearchEquals@akademienl.social) collection […]
It took a while, but now we are gathering contribution reports and present them online as a ResearchEquals (https://fediscience.org/@ResearchEquals@akademienl.social) collection […]
Original post on fediscience.org
fediscience.org
June 2, 2025 at 9:49 AM
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 (https://fediscience.org/@ResearchEquals@akademienl.social) collection […]
It took a while, but now we are gathering contribution reports and present them online as a ResearchEquals (https://fediscience.org/@ResearchEquals@akademienl.social) 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 […]
- 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 […]
Original post on fediscience.org
fediscience.org
March 28, 2025 at 7:57 AM
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 […]
- 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 […]
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. 😉
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. 😉
March 13, 2025 at 8:40 PM
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. 😉
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. 😉