README.md

Overview

snkmt (Snakemate) works with the snakemake-logger-plugin-snkmt plugin to capture and store Snakemake workflow execution data in a SQLite database. This allows you to monitor workflow progress, view job statuses, and troubleshoot errors through an interactive terminal interface.

Note: This project is still under active development. Please report bugs, weird UI behavior, and feature requests - they are greatly appreciated!

How it Works

1. The snakemake-logger-plugin-snkmt plugin captures workflow events during Snakemake execution
2. Events are written to a local SQLite database
3. snkmt provides tools to view and monitor this data through a terminal UI and CLI commands

Installation

Install via the logger plugin (recommended):

pip install snakemake-logger-plugin-snkmt

This will automatically install snkmt as a dependency.

Usage

Execute a Snakemake workflow

snakemake --logger snkmt ...

Interactive Console

Launch the real-time monitoring interface:

• Tab / Shift+Tab: Navigate between interface elements
• Enter: Select workflow rows or log files
• Escape: Close modals/dialogs
• r: Force refresh tables
• h: Hide selected workflow
• u: Unhide all workflows
• d: Delete selected workflow
• Ctrl+P: Open database source selector
• q / Ctrl+C: Quit application

snkmt console

Options:

• --db-path, -d: Specify custom database path
• --refresh-interval, -r: Auto-refresh interval in seconds (default: 1.0, set to 0 to disable — useful for NFS or remote filesystems)

Database Commands

View database information:

snkmt db info [DB_PATH]

Migrate database to latest version:

snkmt db migrate [DB_PATH]

Configuration

By default, snkmt stores data in the XDG Base Directory specified user data directory. You can customize this location using the --db-path option or by configuring the logger plugin.

Screenshots

Main Dashboard

Error Inspection

License

This project is licensed under the MIT License. See the LICENSE file for details.