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.

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=3.12 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:

pip install --upgrade -r requirements-dev.txt -e .

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.