Migrating Legacy Bioinformatics Pipelines to Nextflow at Personalis for Faster Cancer Detection and Monitoring
Read the full case study3x
faster wall-clock runtimes across all products
1000x
reduction in disk space usage
100s
hours per year saved on DevOps workloads
Aim
Build a modular and scalable pipeline infrastructure to accelerate precision oncology R&D, enabling earlier cancer detection and streamlined monitoring, as well as faster, reproducible product delivery.Challenges
- →Continuous iteration on products were needed to keep pace with evolving R&D requirements.
- →Support a unified codebase for major products: ImmunoID NeXT®, NeXT Dx®, and NeXT Personal®.
- →Lack of workflow flexibility hindered modular pipeline development and slowed updates.
- →High maintenance overhead due to tightly coupled dependencies and outdated infrastructure.
— Kate Gerhardt, Senior Bioinformatics Engineer
Solution
Nextflow
Orchestrate modular, containerized pipelines with clear inputs and outputs that communicate via channels for reproducible and scalable analysis.
MultiQC
Compiles analysis results into a single HTML report for easy quality control review.
Docker
Isolates processes to ensure consistent, reproducible execution across environments.
Results
By migrating their legacy scientific workflow system to Nextflow, Personalis was able to build a modular, efficient, and maintainable infrastructure. This transition delivered major performance gains, including 3 times faster wall-clock runtimes across all products and disk space reductions of up to 1000 times. They were also able to streamline DevOps operations, saving hundreds of engineering hours per year through automated deployments.
These improvements not only optimized resource usage but also enhanced reproducibility, maintainability, and research agility, accelerating both development cycles and innovation across the company’s precision oncology platforms.
3x
Opportunity
Advancing cancer tracking and therapy selection:
Detect recurrence earlier and monitor tumor evolution on one platform, enabling faster, data-driven clinical decisions.
Enhance drug development success
Improve patient stratification and increase trial efficiency using proprietary tests and algorithms tailored to drive better outcomes in drug development.
Personalized vaccines at scale
Power individualized neoantigen therapy design and monitor patient-specific immune response with the ImmunoID NeXT® platform.
About
Personalis is a precision oncology company that provides comprehensive insights into tumor and immune biology to advance cancer diagnostics and therapeutics. The Bioinformatics Engineering group, comprising 20 bioinformaticians, is responsible for the development and maintenance of all bioinformatics pipelines at Personalis, and supports around 50 researchers. These pipelines power key products including the ImmunoID NeXT® immunogenomics platform, NeXT Personal® for molecular residual disease (MRD) detection, and NeXT Dx® for solid tumor genomic profiling, as well as internal research and development efforts.
To learn more, visit https://www.personalis.com/