nf-scil

Welcome to nf-scil ! A Nextflow modules and workflows repository for neuroimaging maintained by the SCIL team. The primary focus of the library is to provide pre-built processes and processing sequences for diffusion Magnetic Resonance Imaging, optimized for Nextflow DLS2, based on open-source technologies and made easily available to pipeline's developers through the nf-core framework.

Using modules from nf-scil

To import modules from nf-scil, you first need to install nf-core on your system (can be done simply using pip install nf-core). Once done, nf-scil modules are imported using this command :

nf-core modules \
  --git-remote https://github.com/scilus/nf-scil.git \
  install <category>/<tool>

where you input the <tool> you want to import from the desired <category>. To get a list of the available modules, run :

nf-core modules \
  --git-remote https://github.com/scilus/nf-scil.git \
  list remote

Developing in nf-scil

Dependencies

• Python ≥ 3.8, < 3.13
• Nextflow ≥ 21.04.3

Developer installation

The project uses poetry to manage python dependencies. To install it using pipx, run the following commands :

pip install pipx
pipx ensurepath
pipx install poetry

Note

If the second command above fails, pipx cannot be found in the path. Prepend the second command with $(which python) -m and rerun the whole block.

Once done, install the project with :

poetry install

Loading the project's environment

The project scripts and dependencies can be accessed using :

poetry shell

which will activate the project's python environment in the current shell. To exit the environment, simply enter the exit command in the shell.

Important

Do not use traditional deactivation (calling deactivate), since it does not relinquish the environment gracefully, making it so you won't be able to reactivate it without exiting the shell.

Contributing to nf-scil

If you want to propose a new module to the repository, follow the guidelines in the module creation documentation. we follow standards closely aligned with nf-core, with some exceptions on process atomicity and how test data is handled. Modules that don't abide to them won't be accepted and PR containing them will be closed automatically.

Running tests

Tests are run through nf-core, using the command :

nf-core modules \
  --git-remote https://github.com/scilus/nf-scil.git \
  test <category/tool>

The tool can be omitted to run tests for all modules in a category.