Compi

Compi provides a framework for developing portable, reproducible computational pipelines for research workflows.

Key Features:

• Packaging with compi-dk: compi-dk packages pipelines and their dependencies into Docker images for reproducible execution.
• Docker integration: Supports containerization using Docker to encapsulate runtime environments and dependencies.
• Automatic job scheduling: Provides automatic scheduling and execution of pipeline jobs.
• Logging: Records execution metadata and job logs for provenance and debugging.
• Shell-script-based pipelines: Supports pipelines implemented as shell scripts while supplying workflow engine features.
• Open-source license: Distributed under the Apache License 2.0.

Scientific Applications:

• Reproducible bioinformatics workflows: Implementation of reproducible computational workflows for bioinformatics and related computational research.
• Containerized workflow deployment: Deployment of pipelines as Docker images created with compi-dk for consistent execution environments.
• Batch job execution and monitoring: Execution and monitoring of batch computational jobs using automatic scheduling and logging features.

Methodology:

Pipelines are implemented as shell scripts with automatic job scheduling and logging and can be packaged into Docker images using compi-dk.