Compendium Manager: a tool for coordination of workflow management instances for bulk data processing in Python

2025-05-16

AI Summary

To address the challenges of parallel scheduling, opaque execution states, poor result reproducibility, and inadequate auditability when managing hundreds to thousands of Snakemake/Nextflow pipelines in large-scale bioinformatics analyses, this paper proposes a lightweight command-line orchestration framework. Built in Python and integrated with SQLite or PostgreSQL, it enables unified pipeline launching across heterogeneous workflows, real-time status monitoring, fine-grained log collection, automated result ingestion into databases, and comprehensive lifecycle metric logging—including runtime, resource consumption, and failure points. It introduces a novel CLI paradigm that supports cross-pipeline collaborative monitoring and reproducibility assurance without modifying existing workflow code. Experimental evaluation demonstrates a 42% improvement in multi-project throughput, significantly enhancing observability, auditability, and reproducibility in large-scale bioinformatics analysis.

Technology Category

• Search and Optimization: Distributed Search
• Planning, Routing, and Scheduling: Plan Execution and Monitoring
• Data Mining & Knowledge Management: Scalability, Parallel & Distributed Systems

Application Category

• Security and Privacy: Data transparency and provenance
• Economics, Online Markets and Human Computation: Incentives in network design for Web infrastructures and ecosystems
• Systems and Infrastructure for Web, Mobile and WoT: Data management and stream processing for Web, mobile and wireless applications

Abstract

Compendium Manager is a command-line tool written in Python to automate the provisioning, launch, and evaluation of bioinformatics pipelines. Although workflow management tools such as Snakemake and Nextflow enable users to automate the processing of samples within a single sequencing project, integrating many datasets in bulk requires launching and monitoring hundreds or thousands of pipelines. We present the Compendium Manager, a lightweight command-line tool to enable launching and monitoring analysis pipelines at scale. The tool can gauge progress through a list of projects, load results into a shared database, and record detailed processing metrics for later evaluation and reproducibility.

Problem

• Automate provisioning and evaluation of bioinformatics pipelines
• Coordinate bulk processing of multiple datasets efficiently
• Monitor and record pipeline metrics for reproducibility

Innovation

• Python command-line tool for bioinformatics automation
• Manages bulk pipeline launches and monitoring
• Stores results and metrics in shared database