In case you need more motivation to join the #SnakemakeHackathon2027 in Switzerland: we will get a tour through the exciting physics experiments at the Paul Scherrer Institute.
indico.cern.ch/e/snakemake2...
indico.cern.ch/e/snakemake2...
Snakemake Workshop and Hackathon March 2027
We are excited to announce the Snakemake Workshop and Hackathon 2027, to be held 8-12 March, 2027 at the Paul Scherrer Institute, Switzerland. This event will bring together passionate developers and ...
indico.cern.ch
November 12, 2026 at 9:08 PM
In case you need more motivation to join the #SnakemakeHackathon2027 in Switzerland: we will get a tour through the exciting physics experiments at the Paul Scherrer Institute.
indico.cern.ch/e/snakemake2...
indico.cern.ch/e/snakemake2...
Starting next week on Monday: “Building and Using HPC-Compliant Snakemake Data Analysis Workflows”, organized by the NHR@SouthWest Simulation and Data Lab Life Sciences and Molecular Systems and presented by yours truthfully.
📅 November 16 to 17, 2026
🕒 Daily: 09:00 to 17:00
📍 Venue: Goethe […]
📅 November 16 to 17, 2026
🕒 Daily: 09:00 to 17:00
📍 Venue: Goethe […]
Original post on fediscience.org
fediscience.org
November 9, 2026 at 8:36 AM
Starting next week on Monday: “Building and Using HPC-Compliant Snakemake Data Analysis Workflows”, organized by the NHR@SouthWest Simulation and Data Lab Life Sciences and Molecular Systems and presented by yours truthfully.
📅 November 16 to 17, 2026
🕒 Daily: 09:00 to 17:00
📍 Venue: Goethe […]
📅 November 16 to 17, 2026
🕒 Daily: 09:00 to 17:00
📍 Venue: Goethe […]
Neat new snakemake pipeline from @mufernando.bsky.social for anchor wave for those of you aligning plant genomes: github.com/mufernando/a...
GitHub - mufernando/anchorwave-snakemake
Contribute to mufernando/anchorwave-snakemake development by creating an account on GitHub.
github.com
November 3, 2026 at 3:47 AM
Neat new snakemake pipeline from @mufernando.bsky.social for anchor wave for those of you aligning plant genomes: github.com/mufernando/a...
Remember, if interested, today in Europe's afternoon or the West Coast's early morning we host a #snakemake community meeting.
https://fediscience.org/@snakemake/117530810222233772
https://fediscience.org/@snakemake/117530810222233772
The #snakemake community is resuming its monthly meetings! 🥳
We are going to discuss the development of Snakemake itself, workflow details, plugins, ...
Next meeting right this next Thursday, Nov 5:
- 07:00–08:00 AM PST
- 04:00–05:00 PM CET
- 03:00-04:00 GMT
Details […]
We are going to discuss the development of Snakemake itself, workflow details, plugins, ...
Next meeting right this next Thursday, Nov 5:
- 07:00–08:00 AM PST
- 04:00–05:00 PM CET
- 03:00-04:00 GMT
Details […]
Original post on fediscience.org
fediscience.org
November 5, 2026 at 11:13 AM
Remember, if interested, today in Europe's afternoon or the West Coast's early morning we host a #snakemake community meeting.
https://fediscience.org/@snakemake/117530810222233772
https://fediscience.org/@snakemake/117530810222233772
If you've always had to remember which scripts to run, and in what order, GNU Make is your solution. You write the steps down once in your Makefile and that's it. Similar tools include Task, Snakemake, and targets (only compatible with R).
(2/6)
(2/6)
November 5, 2026 at 4:52 PM
If you've always had to remember which scripts to run, and in what order, GNU Make is your solution. You write the steps down once in your Makefile and that's it. Similar tools include Task, Snakemake, and targets (only compatible with R).
(2/6)
(2/6)
Beep, Beep - I am your friendly #snakemake release announcement bot.
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗪𝗼𝗿𝗸𝗳𝗹𝗼𝘄 𝗥𝘂𝗻 𝗥𝗢-𝗖𝗿𝗮𝘁𝗲 systems. Its version now is 0.1.0!
Give us some time, and you will automatically find the plugin on #pypi […]
[Original post on fediscience.org]
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗪𝗼𝗿𝗸𝗳𝗹𝗼𝘄 𝗥𝘂𝗻 𝗥𝗢-𝗖𝗿𝗮𝘁𝗲 systems. Its version now is 0.1.0!
Give us some time, and you will automatically find the plugin on #pypi […]
[Original post on fediscience.org]
November 3, 2026 at 3:05 PM
Beep, Beep - I am your friendly #snakemake release announcement bot.
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗪𝗼𝗿𝗸𝗳𝗹𝗼𝘄 𝗥𝘂𝗻 𝗥𝗢-𝗖𝗿𝗮𝘁𝗲 systems. Its version now is 0.1.0!
Give us some time, and you will automatically find the plugin on #pypi […]
[Original post on fediscience.org]
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗪𝗼𝗿𝗸𝗳𝗹𝗼𝘄 𝗥𝘂𝗻 𝗥𝗢-𝗖𝗿𝗮𝘁𝗲 systems. Its version now is 0.1.0!
Give us some time, and you will automatically find the plugin on #pypi […]
[Original post on fediscience.org]
Just started using snakemake which feels pretty good for a make/targets system that plays nice with HPC
November 2, 2026 at 5:37 PM
Just started using snakemake which feels pretty good for a make/targets system that plays nice with HPC
Aaand ... #derse27 poster abstract No. 3 submitted. This one together with @fbartusch, @johanneskoester . @egonw and @tkuhn are also on board, because this one is about workflow provenance with #snakemake, #nanopublication and #rocr.
Stay tuned for updates - the conference is in February 2027 […]
Stay tuned for updates - the conference is in February 2027 […]
Original post on fediscience.org
fediscience.org
November 3, 2026 at 7:17 AM
Aaand ... #derse27 poster abstract No. 3 submitted. This one together with @fbartusch, @johanneskoester . @egonw and @tkuhn are also on board, because this one is about workflow provenance with #snakemake, #nanopublication and #rocr.
Stay tuned for updates - the conference is in February 2027 […]
Stay tuned for updates - the conference is in February 2027 […]
Beep, Beep - I am your friendly #snakemake release announcement bot.
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗡𝗮𝗻𝗼𝗽𝘂𝗯𝘀 systems. Its version now is 0.5.1!
Give us some time, and you will automatically find the plugin on #bioconda and #pypi […]
[Original post on fediscience.org]
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗡𝗮𝗻𝗼𝗽𝘂𝗯𝘀 systems. Its version now is 0.5.1!
Give us some time, and you will automatically find the plugin on #bioconda and #pypi […]
[Original post on fediscience.org]
October 31, 2026 at 7:37 AM
Beep, Beep - I am your friendly #snakemake release announcement bot.
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗡𝗮𝗻𝗼𝗽𝘂𝗯𝘀 systems. Its version now is 0.5.1!
Give us some time, and you will automatically find the plugin on #bioconda and #pypi […]
[Original post on fediscience.org]
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗡𝗮𝗻𝗼𝗽𝘂𝗯𝘀 systems. Its version now is 0.5.1!
Give us some time, and you will automatically find the plugin on #bioconda and #pypi […]
[Original post on fediscience.org]
Beep, Beep - I am your friendly #snakemake release announcement bot.
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗡𝗮𝗻𝗼𝗽𝘂𝗯𝘀 systems. Its version now is 0.5.0!
Give us some time, and you will automatically find the plugin on #bioconda and #pypi […]
[Original post on fediscience.org]
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗡𝗮𝗻𝗼𝗽𝘂𝗯𝘀 systems. Its version now is 0.5.0!
Give us some time, and you will automatically find the plugin on #bioconda and #pypi […]
[Original post on fediscience.org]
October 30, 2026 at 7:53 PM
Beep, Beep - I am your friendly #snakemake release announcement bot.
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗡𝗮𝗻𝗼𝗽𝘂𝗯𝘀 systems. Its version now is 0.5.0!
Give us some time, and you will automatically find the plugin on #bioconda and #pypi […]
[Original post on fediscience.org]
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗡𝗮𝗻𝗼𝗽𝘂𝗯𝘀 systems. Its version now is 0.5.0!
Give us some time, and you will automatically find the plugin on #bioconda and #pypi […]
[Original post on fediscience.org]
Some of you out there are #snakemake developers. Next Thursday we resume the series of community meetings! Join us, if you find the time and have development questions - or just for the company.
The #snakemake community is resuming its monthly meetings! 🥳
We are going to discuss the development of Snakemake itself, workflow details, plugins, ...
Next meeting right this next Thursday, Nov 5:
- 07:00–08:00 AM PST
- 04:00–05:00 PM CET
- 03:00-04:00 GMT
Details […]
We are going to discuss the development of Snakemake itself, workflow details, plugins, ...
Next meeting right this next Thursday, Nov 5:
- 07:00–08:00 AM PST
- 04:00–05:00 PM CET
- 03:00-04:00 GMT
Details […]
Original post on fediscience.org
fediscience.org
October 31, 2026 at 7:48 AM
Some of you out there are #snakemake developers. Next Thursday we resume the series of community meetings! Join us, if you find the time and have development questions - or just for the company.
The #snakemake community is resuming its monthly meetings! 🥳
We are going to discuss the development of Snakemake itself, workflow details, plugins, ...
Next meeting right this next Thursday, Nov 5:
- 07:00–08:00 AM PST
- 04:00–05:00 PM CET
- 03:00-04:00 GMT
Details […]
We are going to discuss the development of Snakemake itself, workflow details, plugins, ...
Next meeting right this next Thursday, Nov 5:
- 07:00–08:00 AM PST
- 04:00–05:00 PM CET
- 03:00-04:00 GMT
Details […]
Original post on fediscience.org
fediscience.org
October 30, 2026 at 4:30 PM
The #snakemake community is resuming its monthly meetings! 🥳
We are going to discuss the development of Snakemake itself, workflow details, plugins, ...
Next meeting right this next Thursday, Nov 5:
- 07:00–08:00 AM PST
- 04:00–05:00 PM CET
- 03:00-04:00 GMT
Details […]
We are going to discuss the development of Snakemake itself, workflow details, plugins, ...
Next meeting right this next Thursday, Nov 5:
- 07:00–08:00 AM PST
- 04:00–05:00 PM CET
- 03:00-04:00 GMT
Details […]
Authors published a paper in Biorxiv, they used Snakemake in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
www.biorxiv.org
October 29, 2026 at 12:00 PM
Authors published a paper in Biorxiv, they used Snakemake in the study. Including #RRIDs will make this less ambiguous.
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
SciScore made a table with this resource, see “Automated Services” module (download as csv, xml or #jats) #OpenScience #methodsmatter
Beep, Beep - I am your friendly #snakemake release announcement bot.
There is a new release of the Snakedeploy tool to deploy Snakemake workflows from the snakemake catalog. Its version now is 0.18.1!
Give us some time, and you will automatically find […]
[Original post on fediscience.org]
There is a new release of the Snakedeploy tool to deploy Snakemake workflows from the snakemake catalog. Its version now is 0.18.1!
Give us some time, and you will automatically find […]
[Original post on fediscience.org]
October 28, 2026 at 9:44 AM
Beep, Beep - I am your friendly #snakemake release announcement bot.
There is a new release of the Snakedeploy tool to deploy Snakemake workflows from the snakemake catalog. Its version now is 0.18.1!
Give us some time, and you will automatically find […]
[Original post on fediscience.org]
There is a new release of the Snakedeploy tool to deploy Snakemake workflows from the snakemake catalog. Its version now is 0.18.1!
Give us some time, and you will automatically find […]
[Original post on fediscience.org]
Beep, Beep - I am your friendly #snakemake release announcement bot.
There is a new release of the Snakedeploy tool to deploy Snakemake workflows from the snakemake catalog. Its version now is 0.18.0!
Give us some time, and you will automatically find […]
[Original post on fediscience.org]
There is a new release of the Snakedeploy tool to deploy Snakemake workflows from the snakemake catalog. Its version now is 0.18.0!
Give us some time, and you will automatically find […]
[Original post on fediscience.org]
October 28, 2026 at 9:38 AM
Beep, Beep - I am your friendly #snakemake release announcement bot.
There is a new release of the Snakedeploy tool to deploy Snakemake workflows from the snakemake catalog. Its version now is 0.18.0!
Give us some time, and you will automatically find […]
[Original post on fediscience.org]
There is a new release of the Snakedeploy tool to deploy Snakemake workflows from the snakemake catalog. Its version now is 0.18.0!
Give us some time, and you will automatically find […]
[Original post on fediscience.org]
@moritz_negwer sorry, took a while.
Basically, you need software releases enabled in your GitHub pipeline, e.g. like here https://github.com/snakemake/snakemake-executor-plugin-slurm/blob/main/.github/workflows/release-please.yml
Then a bioconda recipe, to realize a first package. I could […]
Basically, you need software releases enabled in your GitHub pipeline, e.g. like here https://github.com/snakemake/snakemake-executor-plugin-slurm/blob/main/.github/workflows/release-please.yml
Then a bioconda recipe, to realize a first package. I could […]
Original post on fediscience.org
fediscience.org
October 28, 2026 at 2:54 PM
@moritz_negwer sorry, took a while.
Basically, you need software releases enabled in your GitHub pipeline, e.g. like here https://github.com/snakemake/snakemake-executor-plugin-slurm/blob/main/.github/workflows/release-please.yml
Then a bioconda recipe, to realize a first package. I could […]
Basically, you need software releases enabled in your GitHub pipeline, e.g. like here https://github.com/snakemake/snakemake-executor-plugin-slurm/blob/main/.github/workflows/release-please.yml
Then a bioconda recipe, to realize a first package. I could […]
I tried the CLI client BrookLIN yesterday, do you know if an option will become available to get the results as a html/plain text file, instead of a link to the website? I would be interested to add genomerxiv to our snakemake identification pipeline.
October 27, 2026 at 12:48 PM
I tried the CLI client BrookLIN yesterday, do you know if an option will become available to get the results as a html/plain text file, instead of a link to the website? I would be interested to add genomerxiv to our snakemake identification pipeline.
Beep, Beep - I am your friendly #snakemake release announcement bot.
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗡𝗮𝗻𝗼𝗽𝘂𝗯𝘀 systems. Its version now is 0.4.0!
Give us some time, and you will automatically find the plugin on #bioconda and #pypi […]
[Original post on fediscience.org]
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗡𝗮𝗻𝗼𝗽𝘂𝗯𝘀 systems. Its version now is 0.4.0!
Give us some time, and you will automatically find the plugin on #bioconda and #pypi […]
[Original post on fediscience.org]
October 25, 2026 at 4:05 PM
Beep, Beep - I am your friendly #snakemake release announcement bot.
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗡𝗮𝗻𝗼𝗽𝘂𝗯𝘀 systems. Its version now is 0.4.0!
Give us some time, and you will automatically find the plugin on #bioconda and #pypi […]
[Original post on fediscience.org]
There is a new release of the 𝗦𝗻𝗮𝗸𝗲𝗺𝗮𝗸𝗲 𝗥𝗲𝗽𝗼𝗿𝘁𝗲𝗿 𝗣𝗹𝘂𝗴𝗶𝗻 𝗳𝗼𝗿 𝗡𝗮𝗻𝗼𝗽𝘂𝗯𝘀 systems. Its version now is 0.4.0!
Give us some time, and you will automatically find the plugin on #bioconda and #pypi […]
[Original post on fediscience.org]
This is merely a release which integrates #pixi support for the plugin. Such that it will play better with other plugins of the #snakemake ecosystem.
One thing which annoys me: I made a typo. Some time ago. "Easyly" instead of "easily". Now, the fix is in the Changelog comment and the codespell […]
One thing which annoys me: I made a typo. Some time ago. "Easyly" instead of "easily". Now, the fix is in the Changelog comment and the codespell […]
October 25, 2026 at 4:14 PM
This is merely a release which integrates #pixi support for the plugin. Such that it will play better with other plugins of the #snakemake ecosystem.
One thing which annoys me: I made a typo. Some time ago. "Easyly" instead of "easily". Now, the fix is in the Changelog comment and the codespell […]
One thing which annoys me: I made a typo. Some time ago. "Easyly" instead of "easily". Now, the fix is in the Changelog comment and the codespell […]
I gave targets and snakemake a whirl on my cytof/scRNA-seq workflows a while back, but it didn't really gel with me. I now use my repo figtracer (and figrun), which works well for me, but I'm not really building pipelines github.com/david-priest...
GitHub - david-priest/figtracer: Plain-text, git-tracked lab notebook for reproducible bioinformatics — keeps figures in your Markdown notes in sync with the R & Python code that made them, and re-ren...
Plain-text, git-tracked lab notebook for reproducible bioinformatics — keeps figures in your Markdown notes in sync with the R & Python code that made them, and re-renders them headlessly from ...
github.com
October 24, 2026 at 6:30 AM
I gave targets and snakemake a whirl on my cytof/scRNA-seq workflows a while back, but it didn't really gel with me. I now use my repo figtracer (and figrun), which works well for me, but I'm not really building pipelines github.com/david-priest...
This framework pairs LLM agents with Snakemake workflows, generating diverse scRNA-seq analytical strategies and validating each as a plan before parallel execution.
October 22, 2026 at 10:03 AM
This framework pairs LLM agents with Snakemake workflows, generating diverse scRNA-seq analytical strategies and validating each as a plan before parallel execution.
2/3 With this in mind, for my Master's thesis in #Bioinformatics, I developed a genome assembly and repetitive element annotation workflow for plant genomes using #Snakemake.
It was a great opportunity to bring together my interests in #Genomics and transposable elements.
It was a great opportunity to bring together my interests in #Genomics and transposable elements.
October 20, 2026 at 3:22 PM
2/3 With this in mind, for my Master's thesis in #Bioinformatics, I developed a genome assembly and repetitive element annotation workflow for plant genomes using #Snakemake.
It was a great opportunity to bring together my interests in #Genomics and transposable elements.
It was a great opportunity to bring together my interests in #Genomics and transposable elements.
HyARQ: a Snakemake workflow for allele-specific read counting and quality control in F1 hybrids https://www.biorxiv.org/content/10.64898/2026.10.16.759667v1
October 19, 2026 at 10:48 AM
HyARQ: a Snakemake workflow for allele-specific read counting and quality control in F1 hybrids https://www.biorxiv.org/content/10.64898/2026.10.16.759667v1
HyARQ: a Snakemake workflow for allele-specific read counting and quality control in F1 hybrids https://www.biorxiv.org/content/10.64898/2026.10.16.759667v1
October 19, 2026 at 10:48 AM
HyARQ: a Snakemake workflow for allele-specific read counting and quality control in F1 hybrids https://www.biorxiv.org/content/10.64898/2026.10.16.759667v1