Snakemake Logger Plugin - Flowo

A Snakemake logger plugin designed to be used with FlowO for real-time task monitoring, making workflow management simple, interactive, and fun! 🎉

Demo page: flowo online

Important: This plugin is designed to be used together with FlowO and requires FlowO to function correctly. It is not a standalone monitoring tool.

🎈 Features

• Stores Snakemake workflow execution data in PostgreSQL database
• Tracks jobs, rules, files, and errors
• Provides comprehensive logging and monitoring capabilities
• Easy integration with existing Snakemake workflows

💻 Installation

pip install snakemake-logger-plugin-flowo

🔧 Configuration

# To generate the default configuration file, run the following command:
# This will create the default .env configuration file in your $HOME/.config/flowo/ directory.
flowo --generate-config

# After generating the .env file, open it with your preferred text editor to adjust the settings:
vim $HOME/.config/flowo/.env

The following environment variables are available for configuration in the .env file:

• POSTGRES_USER: PostgreSQL username (default: flowo)
• POSTGRES_PASSWORD: PostgreSQL password (default: flowo_password)
• POSTGRES_DB: PostgreSQL database name (default: flowo_logs)
• POSTGRES_HOST: PostgreSQL host (default: localhost)
• POSTGRES_PORT: PostgreSQL port (default: 5432)
• FLOWO_USER: User displayed in Flowo
• FLOWO_WORKING_PATH: Snakemake execution project path

Note: The PostgreSQL database used by this plugin is configured in FlowO. Ensure FlowO is properly set up before using this logger plugin.

🚀 Usage

Basic usage

snakemake --logger flowo

Optional args: logger-flowo-name or logger-flowo-tags

snakemake \
    --logger flowo \
    --logger-flowo-name=your_project_name \
    --logger-flowo-tags="tagA,tagB,tagC"

🙏 Acknowledgement

This project is developed based on the excellent work of cademirch/snakemake-logger-plugin-snkmt. Special thanks to the original author for providing a solid foundation under the MIT License.