AWS HealthOmics now allows customers to specify the Nextflow engine version at run time via the StartRun API, enabling customers to pin runs to a specific Nextflow version for controlled migration. With this launch, customers can select from supported Nextflow versions (22.04, 23.10, 24.10, 25.10, 26.04) through the new engine-settings parameter, giving explicit control at the point of execution. AWS HealthOmics is a HIPAA-eligible service that helps healthcare and life sciences customers accelerate scientific breakthroughs at scale with fully managed bioinformatics workflows.

Nextflow version pinning gives customers full control over when and how they adopt new engine versions. The run-time version override ensures that even when a workflow definition specifies a version via manifest.nextflowVersion in its config or profile, the StartRun API parameter takes precedence, enabling customers to test the same workflow across multiple engine versions without modifying workflow source code. Production workflows can remain on a validated engine version while development teams test newer versions in parallel, reducing the risk of unexpected behavior changes. This is valuable for regulated environments where pipeline validation is required before upgrading to a new engine version.

Nextflow version pinning at run time is now available for Nextflow workflow runs in all AWS HealthOmics regions: US East (N. Virginia), US West (Oregon), Europe (Frankfurt, Ireland, London), Israel (Tel Aviv), and Asia Pacific (Singapore, Seoul). To learn more, visit the Nextflow engine settings documentation.