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.
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:
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
Python Package Index
Install from PyPI:
pip install nf-core
Development version
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
# 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.
Release files for nf-core 4.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| nf_core-4.1.0.tar.gz | 629.9 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| nf_core-4.1.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 1.4 MB
Release files / nf_core-4.1.0.tar.gz
| Download URL | nf_core-4.1.0.tar.gz |
|---|---|
| Size | 629.9 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
| Uploaded via |
twine/6.1.0 CPython/3.13.14
|
Release files / nf_core-4.1.0-py3-none-any.whl
| Download URL | nf_core-4.1.0-py3-none-any.whl |
|---|---|
| Size | 725.8 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.1.0 CPython/3.13.14
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