Accelerating Innovation: Inside the Genomics England Hackathon 2025

Last month, Seqera hosted a hackathon with Genomics England, bringing together bioinformaticians and Nextflow experts to tackle real-world challenges and enhance workflow capabilities. Over 2 days, teams tackled several critical projects, from following nf-core best practices to converting legacy WDL variant calling pipelines to Nextflow. The goal was to accelerate development, build technical confidence, and embed best practices across Genomics England.

Why a Hackathon? The Vision Behind the Event

Genomics England is undertaking a broader initiative to strengthen their internal capability around workflow development and automation. While some team members were advanced Nextflow users, most worked at basic to intermediate levels. Recognizing this gap, a hackathon with Seqera’s Professional Services team offered an ideal opportunity to:

• Upskill bioinformaticians with hands-on Nextflow experience.
• Gain direct access to Seqera, the team behind Nextflow.
• Accelerate the development of in-house data pipelines.
• Foster collaboration and knowledge-sharing across the team.

Key Hackathon Projects

During the hackathon, Genomics England and Seqera worked together to tackle five key projects, each designed with clear objectives, development approaches, and measurable outcomes:

1. Building an internal mirror of the nf-core/modules repository

Genomics England lacked a centralized space for sharing Nextflow modules, causing duplication of development efforts and inconsistent best practices across teams. This exploratory project aimed to establish an nf-core-style internal repository for standardized, discoverable modules.

2. Developing CI for internal Nextflow workflows

Inconsistent CI setups across projects led to the uneven application of quality checks and manual testing, creating slow and error-prone development cycles. The project aimed to create a standardized, reusable CI template that would automate linting, testing, and validation for all Nextflow pipelines.

3. Resolving inter-process metadata dependencies

Pipeline components were tightly coupled to metadata stores for data retrieval, limiting portability and complicating testing since components required a live metadata store connection. This project aimed to design an architectural pattern that decoupled pipeline components from metadata systems, improving flexibility and testability.

4. Modernizing legacy WDL pipelines to Nextflow

Existing WDL workflows ran on outdated orchestration systems with limited parallelization and lacked integration with downstream analysis components. This project aimed to reimplement workflows in Nextflow with improved modularity, parallelization, and comprehensive testing to enhance maintainability and data quality.

5. Enhancing workflows for multi-program support

Existing structural variant workflows were designed for single-cohort processing, with inflexible logic funneling all VCF formats through complex conditional logic in bash scripts. This refactoring project explored separating variant streams with intelligent file routing to support diverse cohort types and processing requirements.

Hackathon Outcomes

The two-day hackathon delivered meaningful progress across all five projects while strengthening collaboration between Genomics England and Seqera. Together, teams tackled real technical challenges and gained practical experience that will inform future workflow development at Genomics England. Here are some key takeaways from the event:

Enhanced Nextflow Expertise

Attendees gained hands-on experience with advanced Nextflow features and modern workflow development approaches. Direct access to Seqera's expertise allowed teams to explore cutting-edge features like lineage tracking and the Nextflow linter, while receiving real-time guidance on architectural decisions and implementation strategies.

"I think the support was great, we received a lot of help from the entire Seqera team, who have helped us understand various features of Nextflow and how we could leverage them to solve our problem." - Hackathon Attendee

Adoption of nf-core Best Practices

The hackathon provided valuable insights into nf-core standards and community-driven best practices. Teams gained a stronger understanding of how to effectively leverage the nf-core framework and discovered they were closer to implementing repositories aligned with nf-core best practices than initially anticipated. They also identified key organizational decisions needed to move forward confidently.

“Having Seqera there to give us advice on best practices, knowledge regarding new features, and the ability to directly discuss potential new features, really contributed to the event's success.” - Hackathon Attendee

Accelerated Development Velocity

The collaborative, in-person format dramatically increased development speed and quality. Teams made tangible progress on complex technical challenges that would typically take weeks or months to resolve. In fact, they achieved 30 pull requests in 2 days (compared to 3 over 3 years) in the WDL-to-Nextflow migration project alone. This acceleration came from combining expert mentorship with focused, uninterrupted development time.

“Personally I learnt a lot of Nextflow (having not used it much before) and we made great progress on migrating an old unmaintainable WDL workflow to a shiny new Nextflow one. The support from Seqera was excellent and helped unblock us on multiple occasions, as well as introducing us to new features we weren't aware of.” - Hackathon Attendee

Strategic Insights for Future Implementations

Beyond immediate technical wins, the hackathon provided crucial strategic clarity. Teams discovered they were closer to implementing repositories similar to nf-core than they originally thought. The event also strengthened the partnership between Genomics England and Seqera, establishing a framework for ongoing collaboration.

“The hackathon was a really useful way to support a mutually beneficial relationship between Seqera and Genomics England. It was great that Seqera staff were there to support exploration of new features like lineage and the Nextflow linter.” - Hackathon Attendee

Reflections and What’s Next

The hackathon demonstrated how focused collaboration with expert support can transform both technical capabilities and team dynamics. Beyond immediate wins, it marked a significant step in Genomics England's initiative to scale internal Nextflow expertise and establish sustainable best practices. As teams build on this foundation, the impact will extend well beyond the two days spent together.

Interested in finding out about our Professional Services offering? Get in touch with the team, or watch our latest on-demand webinar on “Scaling from proof-of-concept to enterprise-wide deployment”.

Meet the Seqera Team in Attendance

Adam Talbot, Scientific Services Lead

Adam Talbot is a Scientific Solutions Lead at Seqera Labs, where he partners with customers to design, build, deploy, and optimize bioinformatics workflows using Nextflow. He specializes in clinical variant calling from cfDNA and has delivered scalable, production-ready pipelines across cloud platforms such as Azure, AWS, and Kubernetes. Adam combines deep technical expertise with hands-on project work to help teams streamline analysis and accelerate discovery.

Harshil Patel, Director of Scientific Development

Harshil has a PhD in Bioinformatics and is an author of over 40 peer-reviewed publications. He has contributed 8 nf-core pipelines which are amongst the most widely used Nextflow pipelines worldwide. He leads a team of bioinformaticians to help Seqera's customers by streamlining their usage of Nextflow and nf-core pipelines via the adoption of Seqera Platform.

Rike Hanssen, Bioinformatics Engineer

Rike is a Bioinformatics Engineer in Seqera’s Scientific Development team, where she supports customers in developing and optimizing bioinformatics workflows with Nextflow. She is an active member of the nf-core community and a lead developer of nf-core/sarek, with contributions to several other open-source pipelines. Prior to joining Seqera, she spent several years building variant calling pipelines and analyzing oncology sequencing data in a core facility setting.

About Genomics England

Genomics England is a global leader in enabling genomic medicine and research, focused on creating a world where everyone benefits from genomic healthcare. Building on the 100,000 Genomes Project, we support the NHS’s world-first national whole genome sequencing service and run the growing National Genomic Research Library, alongside delivering numerous major genomics initiatives such as the Generation Study.

By connecting research and clinical care at national scale, we enable immediate healthcare benefits and advances for the future.