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

There is a new release of Snakemake. Its version now is 9.14.6!

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

If you want to discuss the release, you will find the maintainer 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/v9.14.6 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* create local clone of git repos for source files from hosting providers: https://github.com/snakemake/snakemake/issues/3643
* create potentially missing .snakemake folder in case of very long command lines for spawned jobs: https://github.com/snakemake/snakemake/issues/3894
* make ilp solver enumeration lazy: https://github.com/snakemake/snakemake/issues/3900
* Prevent broken report_href links by using deterministic report IDs with fixed prefix length: https://github.com/snakemake/snakemake/issues/3889
* refactor LoggerManager setup and scope: https://github.com/snakemake/snakemake/issues/3851
* yield proper error message in case a local git source file is not retrievable: https://github.com/snakemake/snakemake/issues/3892

𝐃𝐨𝐜𝐮𝐦𝐞𝐧𝐭𝐚𝐭𝐢𝐨𝐧

* explain how to pass nested config via CLI: https://github.com/snakemake/snakemake/issues/3885

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

There is a new release of Snakemake. Its version now is 9.14.6!

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

If you want to discuss the release, you will find the maintainer 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/v9.14.6 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* create local clone of git repos for source files from hosting providers: https://github.com/snakemake/snakemake/issues/3643
* create potentially missing .snakemake folder in case of very long command lines for spawned jobs: https://github.com/snakemake/snakemake/issues/3894
* make ilp solver enumeration lazy: https://github.com/snakemake/snakemake/issues/3900
* Prevent broken report_href links by using deterministic report IDs with fixed prefix length: https://github.com/snakemake/snakemake/issues/3889
* refactor LoggerManager setup and scope: https://github.com/snakemake/snakemake/issues/3851
* yield proper error message in case a local git source file is not retrievable: https://github.com/snakemake/snakemake/issues/3892

𝐃𝐨𝐜𝐮𝐦𝐞𝐧𝐭𝐚𝐭𝐢𝐨𝐧

* explain how to pass nested config via CLI: https://github.com/snakemake/snakemake/issues/3885

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

There is a new release of Snakemake. Its version now is 9.14.3!

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

If you want to discuss the release, you will find the maintainer 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/v9.14.3 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* ensure that queue input jobs wait if the queue is still empty upon job creation: https://github.com/snakemake/snakemake/issues/3866
* fix issues with cyclic dependencies when using the update and before_update flag: https://github.com/snakemake/snakemake/issues/3857

@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?

@pjacock @maartenk

Just _now_ in #bioconda . Please give it a try, Peter. The execution is skipped in a CI environment. The fact that it passed the Bioconda test makes me optimistic.

As for the documentation page: I have to wait, as I cannot trigger an update. But I will pay attention.

AS for the change: It was a crude hack. See:

https://fediscience.org/@snakemake/115701873440242545

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

There is a new release of the Snakemake executor for #SLURM on #HPC systems. Its version now is 2.0.2!

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

If you want to discuss the release, you will find the maintainers 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/v2.0.2 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* partition cluster selection: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/385

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

There is a new release of the Snakemake executor for #SLURM on #HPC systems. Its version now is 2.0.2!

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

If you want to discuss the release, you will find the maintainers 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/v2.0.2 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* partition cluster selection: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/385

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

There is a new release of Snakemake. Its version now is 9.14.3!

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

If you want to discuss the release, you will find the maintainer 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/v9.14.3 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* ensure that queue input jobs wait if the queue is still empty upon job creation: https://github.com/snakemake/snakemake/issues/3866
* fix issues with cyclic dependencies when using the update and before_update flag: https://github.com/snakemake/snakemake/issues/3857

@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?

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

There is a new release of the Snakemake executor for #SLURM on #HPC systems. Its version now is 2.0.1!

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

If you want to discuss the release, you will find the maintainers 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/v2.0.1 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* validator check for integers was broken.: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/381

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

There is a new release of Snakemake. Its version now is 9.14.0!

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

If you want to discuss the release, you will find the maintainer 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/v9.14.0 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* Support Hy in script directive: https://github.com/snakemake/snakemake/issues/3824

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* Add support for pathlib in `notebook` field: https://github.com/snakemake/snakemake/issues/3811
* Addressed race condition in workdir_handler.py: https://github.com/snakemake/snakemake/issues/3844
* cleanup update-marked output files of failed jobs if there was no backup to restore them: https://github.com/snakemake/snakemake/issues/3843
* correct Windows callable path handling: https://github.com/snakemake/snakemake/issues/3832
* expand env vars on resources: https://github.com/snakemake/snakemake/issues/3823
* fix backup for output marked by `update`: https://github.com/snakemake/snakemake/issues/3839
* Minor fixes/additions to logging module.: https://github.com/snakemake/snakemake/issues/3802
* mount local storage prefix into containers: https://github.com/snakemake/snakemake/issues/3840
* proper...

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

There is a new release of the Snakemake executor for #SLURM on #HPC systems. Its version now is 2.0.1!

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

If you want to discuss the release, you will find the maintainers 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/v2.0.1 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* validator check for integers was broken.: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/381

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

There is a new release of Snakemake. Its version now is 9.14.0!

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

If you want to discuss the release, you will find the maintainer 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/v9.14.0 for details. Here is the header of the changelog:
𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* Support Hy in script directive: https://github.com/snakemake/snakemake/issues/3824

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* Add support for pathlib in `notebook` field: https://github.com/snakemake/snakemake/issues/3811
* Addressed race condition in workdir_handler.py: https://github.com/snakemake/snakemake/issues/3844
* cleanup update-marked output files of failed jobs if there was no backup to restore them: https://github.com/snakemake/snakemake/issues/3843
* correct Windows callable path handling: https://github.com/snakemake/snakemake/issues/3832
* expand env vars on resources: https://github.com/snakemake/snakemake/issues/3823
* fix backup for output marked by `update`: https://github.com/snakemake/snakemake/issues/3839
* Minor fixes/additions to logging module.: https://github.com/snakemake/snakemake/issues/3802
* mount local storage prefix into containers: https://github.com/snakemake/snakemake/issues/3840
* proper...

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

There is a new release of the Snakemake executor for #SLURM on #HPC systems. Its version now is 2.0.0!

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

If you want to discuss the release, you will find the maintainers 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/v2.0.0 for details. Here is the header of the changelog:

𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
⚠ 𝐁𝐑𝐄𝐀𝐊𝐈𝐍𝐆 𝐂𝐇𝐀𝐍𝐆𝐄𝐒

* proposal for dynamic partition selection: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/321

𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬

* partition time handling: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/378
* proposal for dynamic partition selection: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/321

𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* naming SLURM logs, SLURM logs not just "log files": https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/372

𝐃𝐨𝐜𝐮𝐦𝐞𝐧𝐭𝐚𝐭𝐢𝐨𝐧

* Replace incorrect Markdown with a blockquote: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/377

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

There is a new release of Snakemake. Its version now is 9.13.6!

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

If you want to discuss the release, you will find the maintainer 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/v9.13.6 for details. Here is the header of the changelog:

𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* only complain about mixed rules and functions for workflows that are not in a single snakefile; improve internal pathvar error handling: https://github.com/snakemake/snakemake/issues/3829

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

There is a new release of Snakemake. Its version now is 9.13.5!

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

If you want to discuss the release, you will find the maintainer 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/v9.13.5 for details. Here is the header of the changelog:

𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* cache wrapper files and wait for them in case of shared filesystem for sources: https://github.com/snakemake/snakemake/issues/3809
* correctly handle meta-wrapper tag replacement depending on the used snakemake-wrapper release: https://github.com/snakemake/snakemake/issues/3826
* ensure that flags are properly considered for input files before applying path modifiers: https://github.com/snakemake/snakemake/issues/3813
* ensure that tokens are not leaked when paths or uris of source files are logged: https://github.com/snakemake/snakemake/issues/3821
* print secs as numeric in jsonl benchmark format: https://github.com/snakemake/snakemake/issues/3814
* revert breaking change in 9.11.9 disallowing empty input files even when unused: https://github.com/snakemake/snakemake/issues/3810
* shorten report ids: https://github.com/snakemake/snakemake/issues/3822

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

There is a new release of Snakemake. Its version now is 9.13.5!

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

If you want to discuss the release, you will find the maintainer 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/v9.13.5 for details. Here is the header of the changelog:

𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* cache wrapper files and wait for them in case of shared filesystem for sources: https://github.com/snakemake/snakemake/issues/3809
* correctly handle meta-wrapper tag replacement depending on the used snakemake-wrapper release: https://github.com/snakemake/snakemake/issues/3826
* ensure that flags are properly considered for input files before applying path modifiers: https://github.com/snakemake/snakemake/issues/3813
* ensure that tokens are not leaked when paths or uris of source files are logged: https://github.com/snakemake/snakemake/issues/3821
* print secs as numeric in jsonl benchmark format: https://github.com/snakemake/snakemake/issues/3814
* revert breaking change in 9.11.9 disallowing empty input files even when unused: https://github.com/snakemake/snakemake/issues/3810
* shorten report ids: https://github.com/snakemake/snakemake/issues/3822

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

There is a new release of the Snakemake executor for #SLURM on #HPC systems. Its version now is 1.9.2!

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

If you want to discuss the release, you will find the maintainers 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/v1.9.2 for details. Here is the header of the changelog:

𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):
𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬

* logo: https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/367