cpg-flow 0.1.0a8

CPG Flow API for Hail Batch

🐙 CPG Flow

TODO: Badges Will look something like this

📋 Table of Contents

1. 🐙 What is this API ?
2. ✨ Production and development links
3. 🔨 Installation
4. 🚀 Build
5. 🐳 Docker
6. 💯 Tests
7. 🌿 Env variables
8. ☑️ Code analysis and consistency
9. 📈 Releases & Changelog
10. 🎬 GitHub Actions
11. ✨ Misc commands
12. ©️ License
13. ❤️ Contributors

🐙 What is this API ?

Welcome to CPG Flow!

This API provides a set of tools and workflows for managing population genomics data pipelines, designed to streamline the processing, analysis, and storage of large-scale genomic datasets. It facilitates automated pipeline execution, enabling reproducible research while integrating with cloud-based resources for scalable computation.

CPG Flow supports various stages of genomic data processing, from raw data ingestion to final analysis outputs, making it easier for researchers to manage and scale their population genomics workflows.

✨ Production and development links

🌐 Production

The production version of this API is available at api.werewolves-assistant.com.

This API is used by the Werewolves Assistant Web App.

The production server is updated automatically with the latest version of the API when a new release is created. (When a new tag is pushed on the main branch)

🛠️ Development

The development version of this API is available at preprod.api.werewolves-assistant.com.

This API is used by the Werewolves Assistant Web App.

The development server is updated automatically when a commit is pushed on the develop branch.

🔨 Installation

To install this project, you will need to have on your machine :

We recommend to use the node version specified in the .nvmrc file.

If you don't have pnpm installed, you can still use npm for all commands below, but we recommend to use pnpm for faster and more reliable installs.

Then, run the following commands :

# Install dependencies and Husky hooks
pnpm install

# Run the app in dev mode
pnpm run start:dev

The above command will start the app in development mode and watch for changes on local.

You can also run the app in development mode with Docker, more information in the Docker section.

🚀 Build

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🐳 Docker

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🔨 Development mode

To develop on this project first clone the repository. Then use the make init to setup for development. This will install the pre-commit hooks and requirements.

git clone https://github.com/populationgenomics/cpg-flow.git
make init

🚀 Production mode

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🧪 Test mode

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💯 Tests

🧪 Unit and E2E tests

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🥒 Acceptance tests

Click on the badge below 👇 to see the reports.

👽 Mutant testing

You can also check the mutation testing report.

▶️ Commands

Before testing, you must follow the installation steps.

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🌿 Env variables

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☑️ Code analysis and consistency

🔍 Code linting & formatting

In order to keep the code clean, consistent and free of bad TS practices, more than 300 ESLint rules are activated !

Complete list of all enabled rules is available in the .eslintrc.js file.

▶️ Commands

Before linting, you must follow the installation steps.

Then, run the following command

# Lint
pre-commit run --all-files

When setting up local linting for development you can also run the following once:

# Install the pre-commit hook
pre-commit install

🥇 Project quality scanner

Multiple tools are set up to maintain the best code quality and to prevent vulnerabilities:

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📈 Releases & Changelog

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🎬 GitHub Actions

This project uses GitHub Actions to automate some boring tasks.

You can find all the workflows in the .github/workflows directory.

🎢 Workflows

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✨ Misc commands

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©️ License

This project is licensed under the MIT License.

❤️ Contributors

There is no contributor yet. Want to be the first ?

If you want to contribute to this project, please read the contribution guide.