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.

#reproducibleComputing #softwareprovenance #nanopub

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...

RE: https://fediscience.org/@rupdecat/116477850614860143

The #SnakemakeHacksthon2026 was a great experience. Learned so many things and also worked a bit on improving the #Snakemake ecosystem.
The Hackathon's summary preprint is just out, thanks to @rupdecat and all the others.
Looking forward to the 2027 edition.

RE: https://fediscience.org/@biohackrxiv/116477505622903440

Today, we published the summary (as a #BioHackrXiv preprint) of the #SnakemakeHackathon2026 . All the accomplishments which contribute once more to improve the #Snakemake "ecosystem" for #reproducibleResearch & #Dataanalysis .

Many thanks to @egonw from BioHackrXiv for helping us!

"Snakemake Hackathon 2026" https://doi.org/10.37044/osf.io/h6zqj_v1

"Nonetheless, the platform’s continued evolution faces several open challenges: improving core performance on heterogeneous high-performance-computing (HPC) resources, extending the plugin architecture for domain-specific extensions, and lowering the entry barrier for novice users while preserving full reproducibility. Here we report on the Snakemake Hackathon 2026, convened in Munich, Germany (9–13 March 2026) with more than 40 participants representing academia, industry, and national-level research infrastructure." https://index.biohackrxiv.org/2026/04/27/h6zqj.html

#SnakemakeHackathon2026 #biohackathon #snakemake

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 0.1.0!

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/v0.1.0 for details. Here is the header of the changelog:

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 2.6.1!

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/v2.6.1 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* code refactoring: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/451
* handle integer slurm_account values from YAML parsing: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/448

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 🥳

#Snakemake #ReproducibleComputing

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