Release notes

--- /!\ --- BREAKING CHANGES --- /!\ ---

This is a major release which break the compatibility with the code of culebrONT v3 🐍 🐍 📦

refactor: 📦

• culebrONT is now working on snakemake version > v8.0.0

Wrapping: 📦

• a major update of Snakecdysis (for more information see : https://forge.ird.fr/phim/sravel/snakecdysis) changes the command line for installation and running of culebrONT.

==> for more information see the documentation : https://culebront.readthedocs.io/en/latest/

• update of the documentation and the documentation URL have changed : https://culebront.readthedocs.io/en/latest/

--- /!\ --- BREAKING CHANGES --- /!\ ---

This is a major realease which break the compatibility with the code of culebrONT v2 🐍 🐍 📦

tools: 🛠

remove some unmaintained and outdated tools : kat and nanopolish

refactor: ⚡

remove sge parameter remove segmentation for medaka

Report: 📑

brand new repport now with quarto

Environnement: 🏝

new packages version in apptainer and.... a lot of bug fixes

Wrapping: 📦

Snakecdysis offers a straightforward and user-friendly solution for encapsulating your Snakemake workflow, transforming it into a robust bioinformatics tool. Combined with Snakecdysis, your Snakemake workflow is converted into a Python package that can be effortlessly installed and executed on both clusters and laptops. The package generated by Snakecdysis effectively offers a diverse set of tools and functionalities designed for both developers and users.

Thanks to the functionnalities of the snakecdysis package we can now:

• make our code a lot lighter
• manage the version of tools with the command culebront show_tools
• check the installation mode and path of configuration file
• others functionnality for debugging

for more information see : https://forge.ird.fr/phim/sravel/snakecdysis

/!\ WARNING --- CulebrONT v3 is now hosted on the ird forge: https://forge.ird.fr/diade/culebront_pipeline

--> an update of the documentation is comming soon