Rnaseq Nextflow pipeline

The Precision Medicine Center was processing hundreds of RNA-seq samples monthly using manual, error-prone workflows. They needed a scalable, reproducible pipeline that could handle varying sample types, ensure quality control, and integrate with their existing infrastructure while maintaining compliance with regulatory standards.

We developed a comprehensive Nextflow pipeline that automates the entire RNA-seq analysis workflow. The pipeline includes quality control, read alignment, quantification, differential expression analysis, and functional annotation. It features automatic resource management, error handling, resume capabilities, and generates comprehensive reports. The solution is containerized using Docker and can run on various compute environments.