Watchdog

Watchdog manages and executes automated, distributed bioinformatics workflows for high-throughput data analysis such as next-generation sequencing (e.g., RNA-seq).

Key Features:

• Automated Workflow Execution: Executes complex, interdependent analysis workflows across multiple samples and conditions to enable reproducible and reusable analyses.
• Platform Independence: Implemented in Java to operate across diverse computing environments.
• Distributed Computing Support: Distributes tasks across multiple compute nodes to process large datasets.
• Customizable Error Detection and Intervention: Provides customizable error detection mechanisms and supports intervention during workflow execution.
• Module Creation and Reusability: Enables semi-automatic module creation from software help pages and supports reusable module definitions.
• Sharing Repositories: Supports repositories for sharing modules and workflows among users.
• Logging and Provenance Capture: Records extensive logs including module and software versions for provenance tracking.
• Package Manager and Container Support: Integrates package managers and container virtualization to ensure consistent execution environments.
• Execution Modes: Supports resuming workflows after interruptions without re-running unaffected tasks and detaching/reattaching to executions while cluster processing continues.

Scientific Applications:

• Next-generation sequencing analysis: Processes NGS datasets including RNA-seq experiments.
• Large-scale experimental data workflows: Manages automated analyses and integration of diverse, large-scale experimental datasets.
• Reproducible bioinformatics analyses: Enables reproducible computational analyses through logging, containerization, and package manager integration.

Methodology:

Implemented in Java; executes automated, distributed workflows; supports semi-automatic module creation from software help pages; captures extensive logs including module and software versions; provides explicit support for package managers and container virtualization; supports resuming execution and detaching/reattaching.