BioNextflow is a collection of modules and sub-workflows that can be used in any Nextflow DSL2 pipeline. They are created with the idea in mind of having a single file per tool, containing different sub-workflows and modules.
The version v3.0 follows the rules from nf-core (less strict).
General functions are placed in global_functions.nf file and can be called from modules / subworkflows.
The modules can be downloaded and used as they are or can be embedded as submodules.
To embed the submodules you can do:
git submodule add https://github.com/biocorecrg/BioNextflow3
...
Cloning into 'BioNextflow'...
remote: Enumerating objects: 636, done.
remote: Counting objects: 100% (306/306), done.
...then you can add the .gitmodule file that is generated:
git add .gitmodules
git commit -m "adding modules"
git pushYou can upgrade the submodules using this command
git submodule update --remote --merge
git add BioNextflow3
git commit -m "upgrading bioNextflow"
git push