rOpenSci will be participating in @latinr_conf!

Here is the key data for your participation:

🎙️ Keynotes

- Heather Turner: Lowering Barriers to Contributing to R.

- Stephanie Zimmer: Transforming a team to open-source first.

- TRACE-LAC Team. Lo invisible del código abierto: Lecciones desde el proyecto TRACE-LAC / Epiverso para conectar el desarrollo de software con la salud pública

🎓 Tutorials by rOpenSci members:

📌 ¡Miércoles, Git! Manejo de errores en Git y no morir en el intento — @maelle , @yabellini. Registration: https://www.eventbrite.cl/e/miercoles-git-manejo-de-errores-en-git-y-no-morir-en-el-intento-tickets-1937068908249

📌 Introducción a #Tidymodels — Francisco Cardozo & Edgar Ruiz. Registration: https://www.eventbrite.cl/e/introducion-a-tidymodels-tickets-1962543491413

📌 Automatización de workflows en R y Python con #targets y #Snakemake — Diana García. Registration: https://www.eventbrite.cl/e/automatizacion-de-workflows-en-r-y-python-con-targets-y-snakemake-tickets-1936131664929

📌 ¿Qué historia vas a contar hoy Herramientas para una comunicación eficaz — Alejandra Bellini. Registration: https://www.eventbrite.cl/e/que-historia-vas-a-contar-hoy-herramientas-para-una-comunicacion-eficaz-tickets-1891497192019

📌 Coding with #AI in RStudio — Juan Cruz Rodríguez & @LuisDVerde. Registration: https://www.eventbrite.cl/e/coding-with-ai-in-rstudio-tickets-1962817615325

List with all tutorials here: https://latinr.org/en/

#RStats #RStatsES #openScience #RSE #OpenData #FOSS #DataScience #Analytics

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rOpenSci will be participating in @latinr_conf!

Here is the key data for your participation:

🎙️ Keynotes

- Heather Turner: Lowering Barriers to Contributing to R.

- Stephanie Zimmer: Transforming a team to open-source first.

- TRACE-LAC Team. Lo invisible del código abierto: Lecciones desde el proyecto TRACE-LAC / Epiverso para conectar el desarrollo de software con la salud pública

🎓 Tutorials by rOpenSci members:

📌 ¡Miércoles, Git! Manejo de errores en Git y no morir en el intento — @maelle , @yabellini. Registration: https://www.eventbrite.cl/e/miercoles-git-manejo-de-errores-en-git-y-no-morir-en-el-intento-tickets-1937068908249

📌 Introducción a #Tidymodels — Francisco Cardozo & Edgar Ruiz. Registration: https://www.eventbrite.cl/e/introducion-a-tidymodels-tickets-1962543491413

📌 Automatización de workflows en R y Python con #targets y #Snakemake — Diana García. Registration: https://www.eventbrite.cl/e/automatizacion-de-workflows-en-r-y-python-con-targets-y-snakemake-tickets-1936131664929

📌 ¿Qué historia vas a contar hoy Herramientas para una comunicación eficaz — Alejandra Bellini. Registration: https://www.eventbrite.cl/e/que-historia-vas-a-contar-hoy-herramientas-para-una-comunicacion-eficaz-tickets-1891497192019

📌 Coding with #AI in RStudio — Juan Cruz Rodríguez & @LuisDVerde. Registration: https://www.eventbrite.cl/e/coding-with-ai-in-rstudio-tickets-1962817615325

List with all tutorials here: https://latinr.org/en/

#RStats #RStatsES #openScience #RSE #OpenData #FOSS #DataScience #Analytics

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@pjacock @egonw @yokofakun

Perhaps a missing postfix?

Anyway, the rolling #Snakemake paper received a non-functional DOI, which was corrected several weeks after the update.

So, perhaps a mix of both? Some email snafu and new DOIs being registered?

@davelunt

Oh, I am dealing with plenty of quirky programs myself. And I hate it. 😉

In the off-chance that this might be new: there is the #Snakemake wrapper project, with plenty of wrappers to make a programmer's life easier. See https://snakemake-wrappers.readthedocs.io/en/stable/

This took a while. After the new version of the Snakemake paper (a rolling paper on F1000) came out, the DOI now is "working" 🥳 :

https://doi.org/10.12688/f1000research.29032.3

From my point of view, it particularly describes the working with various #HPC batch systems. And: Development did not cease. If you want to follow our announcement bot for updates: @snakemake

#Snakemake #ReproducibleComputing #DataAnalysis #OpenScience #WorkflowManagement

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

@davelunt just stumbled over the #Snakemake hashtag. Snakemake has the directory() function just for that purpose: https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#directories-as-outputs

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

Just submitted a talk for FOSDEM (been invited). They asked to attach an icon-image for the talk. So I drew one. The compute racks are difficult to identify as such, but this is as far as my aquarelle skills go.

#Snakemake #ReproducibleComputing #HPC

Just getting back from two day course teaching #Snakemake programming on #HPC clusters. And I have several observations:

- the education level everywhere else seems way better, than on my home cluster. It is still a good idea, to assume the worst.
- it is never a good idea to accept bring-your-own-device: The Windows users with their tiny laptops will always have connection issues to a HPC system and will be working with one terminal (and usually tiny fonts).
- Some kind of IDE, common for all on decent screens, is a minimum. There are several options.
- clusters with QOS settings (quality of service) are confusing for some, because it is of course confusing to have a new obscure flag, when you are digesting a dozen other learning items.
- I need to fix a few things 😊

And most of all: I really need to start conceptualizing a smaller workshop, “bring your workflow, and we will port it to this system”. A new PR to the #SLURM plugin might help to ease the partition selection ...

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

My current #bioinformatics peeve: programs that don’t allow me to specify the output file names, or only the stub but then add filename suffixes. Not good citizens. Makes it really hard to use in workflows as filenames magically appear ! #snakemake