# cg
![Build Status - Github][gh-actions-badge]
[![Coverage Status][coveralls-image]][coveralls-url]
[![GitHub issues-closed][closed-issues-img]][closed-issues-url]
[![Average time to resolve an issue][ismaintained-resolve-img]][ismaintained-resolve-url]
[![Percentage of issues still open][ismaintained-open-rate-img]][ismaintained-open-rate-url]
[![CodeFactor][codefactor-badge]][codefactor-url]
[![Code style: black][black-image]][black-url]
`cg` stands for _Clinical Genomics_; a clinical sequencing platform under [SciLifeLab][scilife]
In this context, `cg` provides the interface between these tools to facilitate automation and other necessary cross-talk. It also exposes some APIs:
- HTTP REST for powering the web portal: [clinical.scilifelab.se][portal]
- CLI for interactions on the command line
### Contributing
Please check out our [guide for contributing to cg](CONTRIBUTING.md)
## Installation
Cg written in Python 3.9+ and is available on the [Python Package Index][pypi] (PyPI).
```bash
pip install cg
```
If you would like to install the latest development version, use [poetry](https://python-poetry.org/docs/).
```bash
git clone https://github.com/Clinical-Genomics/cg
cd cg
poetry install
```
[portal]: https://clinical.scilifelab.se/
[trailblazer]: https://github.com/Clinical-Genomics/trailblazer
[housekeeper]: https://github.com/Clinical-Genomics/housekeeper
[genotype]: https://github.com/Clinical-Genomics/genotype
[scilife]: https://www.scilifelab.se/
[pypi]: https://pypi.org/
[black]: https://black.readthedocs.io/en/stable/
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[coveralls-image]: https://coveralls.io/repos/github/Clinical-Genomics/cg/badge.svg?branch=master
[gh-actions-badge]: https://github.com/Clinical-Genomics/cg/workflows/Tests%20and%20coveralls/badge.svg
[closed-issues-img]: https://img.shields.io/github/issues-closed/Clinical-Genomics/cg.svg
[closed-issues-url]: https://GitHub.com/Clinical-Genomics/cg/issues?q=is%3Aissue+is%3Aclosed
[ismaintained-resolve-img]: http://isitmaintained.com/badge/resolution/Clinical-Genomics/cg.svg
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[codefactor-url]: https://www.codefactor.io/repository/github/clinical-genomics/cg
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[black-url]: https://github.com/psf/black
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