Nextflow is one of the most widely used workflow management tools in bioinformatics. Seqera Platform builds on top of Nextflow and provides a user-friendly interface to share pipelines, deploy them on major cloud providers (in our case, Google Cloud Platform), access results, and manage execution at scale.

To be honest, when we first looked into the Seqera Platform (Nextflow), we were skeptics. As a computational team at ALLOX, we already had our ways of organizing pipelines and sharing data. We wondered: Do we really need another layer?

Six months later, the answer is a resounding yes – it has completely transformed our work. Here are three aspects that turned out to be game-changers:

🚀 Empowering Users

Seqera Platform democratizes access to compute power. Team members with expertise in very different technical domains can now run complex bioinformatics pipelines.

This gives the lab team more control over the data they generate and helps them plan experiments more efficiently. Previously, many experimental steps depended on the compute team preparing and running analyses before the lab could move forward; now much of that bottleneck is gone. The lab team loves it!

🛠️ Simplifying Support

Support and debugging became much easier. When users run pipelines, the compute team can see all the inputs, configurations, and execution history, making every run fully reproducible.

This reduced endless back-and-forth messages and even made some of our dedicated Slack support channels suspiciously quiet. Instead of chasing configuration issues, we can now focus on building new pipelines and doing more interesting analyses.

☁️ Portable, Scalable Pipelines

Seqera Platform + Nextflow abstracts complex pipeline logic into scripts that are fairly easy to write. With minor adjustments, the same pipeline can run on a laptop, an HPC cluster, or the cloud.

Cloud support (especially GCP in our case) has been a massive win. Pipelines that would have been an engineering headache with raw Bash scripts or JSON batch submissions become straightforward in Nextflow. We can focus on logic, data, and hypotheses instead of compatibility issues, container setup, and resource provisioning.

The productivity gains and time savings were so clear that we’re doubling down – growing the ALLOX compute team to push our platform even further.

The ALLOX tech stack enables deep integration between teams.