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<source media="(prefers-color-scheme: dark)" srcset="https://raw.githubusercontent.com/nf-core/tools/main/docs/images/nfcore-tools_logo_dark.png">
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[](https://github.com/nf-core/tools/actions?query=workflow%3A%22Python+tests%22+branch%3Amain)
[](https://codecov.io/gh/nf-core/tools)
[](https://github.com/prettier/prettier)
[](https://github.com/charliermarsh/ruff)
[](https://bioconda.github.io/recipes/nf-core/README.html)
[](https://pypi.org/project/nf-core/)
[](https://nfcore.slack.com/channels/tools)
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](https://nf-co.re/tools/docs/).
## Installation
For full installation instructions, please see the [nf-core documentation](https://nf-co.re/docs/nf-core-tools/installation).
Below is a quick-start for those who know what they're doing:
### Bioconda
Install [from Bioconda](https://bioconda.github.io/recipes/nf-core/README.html):
```bash
conda install nf-core
```
Alternatively, you can create a new environment with both nf-core/tools and nextflow:
```bash
conda create --name nf-core python=3.12 nf-core nextflow
conda activate nf-core
```
### Python Package Index
Install [from PyPI](https://pypi.python.org/pypi/nf-core/):
```bash
pip install nf-core
```
### Development version
```bash
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:
```bash
pip install --upgrade -r requirements-dev.txt -e .
```
## Contributions and Support
If you would like to contribute to this package, please see the [contributing guidelines](.github/CONTRIBUTING.md).
For further information or help, don't hesitate to get in touch on the [Slack `#tools` channel](https://nfcore.slack.com/channels/tools) (you can join with [this invite](https://nf-co.re/join/slack)).
## 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](https://dx.doi.org/10.1038/s41587-020-0439-x).
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