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 2.7.0!

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/v2.7.0 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* cpu jobs skip gpu partitions: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/454

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* [#446]: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/446
* pipeline hangs when submitting from compute nodes: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/450
* relaxed dependencies: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/460

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

There is a new release of Snakemake. Its version now is 9.21.0!

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/v9.21.0 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* add a function to help with prepending arguments to filenames; close [#672]: https://github.com/snakemake/snakemake/issues/672, https://github.com/snakemake/snakemake/issues/4090

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* close plugin handlers after draining QueueListener in LoggerManager.stop: https://github.com/snakemake/snakemake/issues/4137

𝐏𝐞𝐫𝐟𝐨𝐫𝐦𝐚𝐧𝐜𝐞 𝐈𝐦𝐩𝐫𝐨𝐯𝐞𝐦𝐞𝐧𝐭𝐬

* adjust default sqlite PRAGMAs, auto detect network fstype: https://github.com/snakemake/snakemake/issues/4152

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 0.2.0!

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

This plugin is relevant for Snakemake users willing to publish
Software Metadata easyly.
The maintainer is here on Mastodon @rupdecat.

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

See https://github.com/snakemake/snakemake-report-plugin-nanopub/releases/tag/v0.2.0 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* added pyaml deps ([a40892c](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/a40892c5c855d26d39fcefb6736accee78f36afc))

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* catching additional ([559bea1](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/559bea1f7eeed3ae9b52e94f86ce117951a6214b))
* formatting ([e054733](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/e0547333f2c4fdfa098f6c4c2295c09a47fd026a))
* formatting & linting ([721bd9d](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/721bd9dc97530cb8dbda16c84017842e517cfe9b))
* now conda env versions are present, so are wrapper versions ([d11ce70](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/d11ce70971848bb6fc24ee114bbd59454ebdb7a4))
* rule info from job stats to rule m...

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

There is a new release of Snakemake. Its version now is 9.20.0!

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/v9.20.0 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* add a helper function that translate Python script names into corresponding module names: https://github.com/snakemake/snakemake/issues/4065
* add with_suffix argument to subpath helper function, allowing low-code suffix extensions and replacements for input and output files and params: https://github.com/snakemake/snakemake/issues/4156
* enable caching for named multi-output rules: https://github.com/snakemake/snakemake/issues/4151

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* CLI/profile runtime override is interpreted as minutes not as seconds: https://github.com/snakemake/snakemake/issues/4053
* **docs:*: https://github.com/snakemake/snakemake/issues/4173
* ensure that also storage plugins without settings are auto-deployed: https://github.com/snakemake/snakemake/issues/4178
* issue 3958 relative path for storage prefix breaks apptainer: https://github.com/snakemake/snakemake/issues/3962
* suppress duplicate SpawnedJobError tracebacks in local executor: https://gith...

X-post from Bluesky:

🧑‍💻Satellite Hackathon at #ViBioM2026!

Join the #Virus #Bioinformatics + @nf_core Hybrid Collaborative #Hackathon & collaborate on bioinformatic tools and ideas & contribute to reproducible workflows & research infrastructure.

Want to write nf-core modules for virus tools? Convert viral analysis workflows to #Nextflow? Add tools to #bioconda ? Contribute VirJenDB? Or your own project?

(supported by @NFDI4Microbiota )

Register your interest 👇

https://evbc.uni-jena.de/events/vibiom2026/hackathon-satellite-event/

This cannot be:

I am trying to compile a few stats for the #Snakemake executor plugin for #SLURM on #HPC systems. Preparing for a lighting talk at the #SnakemakeHackathon2026

PyPi: 20,000 downloads last month
BioConda: > 60,000 total (aggregated over all versions)

Impressive as it might be, this is contradictory. PyPi would exceed BioConda by a huge margin.

Does anyone know how to get all-time statistics from either platform? #BioConda or #PyPi?

CondaNest – GUI quản lý môi trường Conda trên Linux, phù hợp cho xử lý đa môi trường Bioconda. Giao diện nhẹ, trực quan, không cần activate để xem gói. Tạo, xóa, dọn dẹp môi trường dễ dàng. Viết bằng Python & GTK4, hiệu năng cao. Đang ở giai đoạn beta – góp ý để cải thiện! #Conda #Bioconda #Linux #Python #GTK4 #OpenSource #conda #bioconda #linux #opensource

https://www.reddit.com/r/opensource/comments/1qi9ewg/i_built_a_native_linux_gui_to_organize_conda/

@egonw a few days ago, I bumped the #Bioconda package of r-wikipathways to v1.30 . Thank you for this wonderful package!

Today, after quite some tinkering, I managed to overlay differential expression results. This is not stable code, yet. The enrichment is a bit fiddly and the overlay relies on finding the right offsets in a downloaded path figure. But perhaps, I am naive and there is a better way?