BEEP, BEEP - I am your friendly #Snakemake release announcement bot.

There is a new release of Snakemake. Its version now is 9.19.0!

Give us some time, and you will automatically find it on #Bioconda and #Pypi.

The maintainer is here on Mastodon -
@johanneskoester .

If you discover any issues, please report them on https://github.com/snakemake/snakemake/issues.

See https://github.com/snakemake/snakemake/releases/tag/v9.19.0 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* clean up profile handling, switch to `profile.yaml` as default file name, allow specifying yaml file instead of dir: https://github.com/snakemake/snakemake/issues/4087

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* avoid race conditions in wrapper/script/notebook retrieval; better error messages for missing wrappers; introduction of DAGProcessorBase for modularization of DAG processing code: https://github.com/snakemake/snakemake/issues/4133

𝐃𝐨𝐜𝐮𝐦𝐞𝐧𝐭𝐚𝐭𝐢𝐨𝐧

* update installation instuctions: https://github.com/snakemake/snakemake/issues/4025

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

Beep, Beep - I am your friendly #Snakemake release announcement bot.

There is a new release of the 𝐒𝐧𝐚𝐤𝐞𝐦𝐚𝐤𝐞 𝐄𝐱𝐞𝐜𝐮𝐭𝐨𝐫 𝐏𝐥𝐮𝐠𝐢𝐧 𝐟𝐨𝐫 𝐒𝐋𝐔𝐑𝐌 systems. Its version now is 2.6.0!

Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.

This plugin is relevant for #HPC users using the #SLURM batch system.
The maintainers are here on Mastodon -
@rupdecat and @johanneskoester.

If you discover any issues, please report them on https://github.com/snakemake/snakemake-executor-plugin-slurm/issues.

See https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v2.6.0 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* job arrays: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/174
* Set tmpspace with help of gres="tmpspace:10G" syntax: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/444

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* logo: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/439

𝐃𝐨𝐜𝐮𝐦𝐞𝐧𝐭𝐚𝐭𝐢𝐨𝐧

* add admin documentation: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/436

BEEP, BEEP - I am your friendly #Snakemake release announcement bot.

There is a new release of Snakemake. Its version now is 9.18.2!

Give us some time, and you will automatically find it on #Bioconda and #Pypi.

The maintainer is here on Mastodon -
@johanneskoester .

If you discover any issues, please report them on https://github.com/snakemake/snakemake/issues.

See https://github.com/snakemake/snakemake/releases/tag/v9.18.2 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* remove debug code ([ac5ad20](https://github.com/snakemake/snakemake/commit/ac5ad209e00aeca2d38e5e5d6ac7f930d2c6a93e))

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

BEEP, BEEP - I am your friendly #Snakemake release announcement bot.

There is a new release of Snakemake. Its version now is 9.18.1!

Give us some time, and you will automatically find it on #Bioconda and #Pypi.

The maintainer is here on Mastodon -
@johanneskoester .

If you discover any issues, please report them on https://github.com/snakemake/snakemake/issues.

See https://github.com/snakemake/snakemake/releases/tag/v9.18.1 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* add pip dependency to publish task ([ea2b5c9](https://github.com/snakemake/snakemake/commit/ea2b5c9708792c9261ded758cc859ce8e18e956b))

BEEP, BEEP - I am your friendly #Snakemake release announcement bot.

There is a new release of Snakemake. Its version now is 9.18.0!

Give us some time, and you will automatically find it on #Bioconda and #Pypi.

The maintainer is here on Mastodon -
@johanneskoester .

If you discover any issues, please report them on https://github.com/snakemake/snakemake/issues.

See https://github.com/snakemake/snakemake/releases/tag/v9.18.0 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* use checksums reported by storage plugins for between workflow caching: https://github.com/snakemake/snakemake/issues/4098

BEEP, BEEP - I am your friendly #Snakemake release announcement bot.

There is a new release of Snakemake. Its version now is 9.17.3!

Give us some time, and you will automatically find it on #Bioconda and #Pypi.

The maintainer is here on Mastodon -
@johanneskoester .

If you discover any issues, please report them on https://github.com/snakemake/snakemake/issues.

See https://github.com/snakemake/snakemake/releases/tag/v9.17.3 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* add curl when containerize with wrapper: https://github.com/snakemake/snakemake/issues/4115
* ensure proper wrapper prefix is passed to CWL and shown in wrapper error messages: https://github.com/snakemake/snakemake/issues/4121
* ensure that strings that purely contain integers or floats: https://github.com/snakemake/snakemake/issues/4119
* incorrect highlighting in HTML report: https://github.com/snakemake/snakemake/issues/4120

𝐃𝐨𝐜𝐮𝐦𝐞𝐧𝐭𝐚𝐭𝐢𝐨𝐧

* document an accidental: https://github.com/snakemake/snakemake/issues/4116
* Rework tutorial: https://github.com/snakemake/snakemake/issues/4068

BEEP, BEEP - I am your friendly #Snakemake release announcement bot.

There is a new release of Snakemake. Its version now is 9.17.2!

Give us some time, and you will automatically find it on #Bioconda and #Pypi.

The maintainer is here on Mastodon -
@johanneskoester .

If you discover any issues, please report them on https://github.com/snakemake/snakemake/issues.

See https://github.com/snakemake/snakemake/releases/tag/v9.17.2 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* **docs:*: https://github.com/snakemake/snakemake/issues/4073
* ensure that the snakemake-wrappers repo is properly cached when --wrapper-prefix is not specified: https://github.com/snakemake/snakemake/issues/4111

𝐃𝐨𝐜𝐮𝐦𝐞𝐧𝐭𝐚𝐭𝐢𝐨𝐧

* prepare redirects in docs: https://github.com/snakemake/snakemake/issues/4106

Geez I hate #LLM #AI showing up at the top of my search results. I was looking up the #SnakeMake command page to remind myself of the syntax for latency waiting for files.

I search. The first result is #AI generated and claims there is no latency command in #SnakeMake. The first real result was the command syntax page. Which detailed the --latency-wait command. Which has existed in the command list for a *LONG* time. 🙄