A python package with helper tools for the nf-core community.

The nf-core tools package is written in Python and can be imported and used within other packages. For documentation of the internal Python functions, please refer to the nf-core tools Python API docs.

For full installation instructions, please see the nf-core documentation. Below is a quick-start for those who know what they're doing:

Install from Bioconda:

conda install nf-core

Alternatively, you can create a new environment with both nf-core/tools and nextflow:

conda create --name nf-core python=3.14 nf-core nextflow
conda activate nf-core

Install from PyPI:

pip install nf-core

pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev

If editing, fork and clone the repo, then install as follows:

uv sync --all-extras

# Activate the virtual environment
source .venv/bin/activate

# Or use uv run to run commands without activating
uv run nf-core --help

If you would like to contribute to this package, please see the contributing guidelines.

For further information or help, don't hesitate to get in touch on the Slack #tools channel (you can join with this invite).

If you use nf-core tools in your work, please cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.