cg 20.0.1

Clinical Genomics command center

cg

cg stands for Clinical Genomics; a clinical sequencing platform under SciLifeLab

This is our main package for interacting with data and samples that flow through our pipeline. We rely on a set of specialized "apps" to deal with a lot of complexity like:

• Trailblazer: Python wrapper around [MIP][mip], a rare disease genomics pipeline
• Housekeeper: storage, retrieval, and archival of files
• Genotype: managing genotypes for detecting sample mix-ups

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
• CLI for interactions on the command line

Contributing

Please check out our guide for contributing to cg

Installation

Cg written in Python 3.6+ and is available on the Python Package Index (PyPI).

pip install cg

If you would like to install the latest development version:

git clone https://github.com/Clinical-Genomics/cg
cd cg

To install CG either use pipenv (as described in contributing) and run

pipenv install -e .

or (without pipenv)

pip install -r requirements-dev.txt --editable .

Files will be blacked automatically with each push to github. If you would like to automatically Black format your commits on your local machince:

pre-commit install