Pathogen Repo Guide

Tip

Follow the Nextstrain tutorial series for Creating a pathogen repository to use the pathogen repo guide as the starting point for a new pathogen repository.

This is a Nextstrain pathogen repository guide for setting up a pathogen repo to hold the files necessary to run and maintain a Nextstrain pathogen build.

Using this guide will allow you to start with the general repository and workflow organization that is expected of a Nextstrain maintained pathogen. However, the workflows will require customizations to support your specific pathogen and should not be expected to "just work".

Working on this repo

This repo is configured to use pre-commit, to help automatically catch common coding errors and syntax issues with changes before they are committed to the repo.

If you will be writing new code or otherwise working within this repo, please do the following to get started:

1. install pre-commit by running either python -m pip install pre-commit or brew install pre-commit, depending on your preferred package management solution
2. install the local git hooks by running pre-commit install from the root of the repo
3. when problems are detected, correct them in your local working tree before committing them.

Note that these pre-commit checks are also run in a GitHub Action when changes are pushed to GitHub, so correcting issues locally will prevent extra cycles of correction.