Tools

<h1> <picture> <source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/nf-core/tools/main/docs/images/nfcore-tools_logo_dark.png"> <img alt="nf-core/tools" src="https://raw.githubusercontent.com/nf-core/tools/main/docs/images/nfcore-tools_logo_light.png"> </picture> </h1><!-- omit in toc -->

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 Tools Python API docs.

Installation

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

Bioconda

Install from Bioconda:

bashCopy
conda install nf-core

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

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

Python Package Index

Install from PyPI:

bashCopy
pip install nf-core

Development version

bashCopy
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:

bashCopy
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

Contributions and Support

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).

Citation

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.