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Seqera Enterprise v25.3.1

Seqera Enterprise

Bug fixes​

Compute environments​

  • Resolved an issue with long-running jobs and sts caching.

Nextflow​

Nextflow upgraded to 25.10.2​

Seqera Platform 25.3.1 includes Nextflow 25.10.2 (previously 25.04.8).

According to the 25.10.0, 25.10.1, and 25.10.2 release notes, there are breaking changes for AWS configurations and the deprecated Google Life Sciences executor. However, existing pipelines will continue to work. New recommended syntax is now available:

New features:

  • Workflow params: New params block for declaring pipeline parameters with type annotations (requires strict syntax)
  • Workflow outputs out of preview: Workflow outputs are now production-ready (remove nextflow.preview.output flag if using)
  • Type annotations: Support for type annotations on parameters, workflows, processes, and functions (requires strict syntax)
  • Auth and Launch commands: New nextflow auth and nextflow launch commands for Seqera Platform integration

Enhancements:

  • Nextflow plugin registry for more efficient plugin downloads
  • Simpler syntax for workflow handlers (onComplete, onError sections in workflows)
  • Simpler syntax for dynamic directives (no closure required with strict syntax)
  • Configurable date formatting via NXF_DATE_FORMAT environment variable

Breaking changes:

  • google-lifesciences executor removed (use google-batch instead)
  • AWS Java SDK upgraded from v1 to v2 (affects aws.client config options)
  • Package nextflow.config.schema renamed to nextflow.config.spec

See the Nextflow 25.10 migration guide for full details.

Note: The default Nextflow version can be overridden by setting NXF_VER in a pre-run script:

export NXF_VER=25.04.8

Nextflow launcher image​

If you host your nf-launcher container image on a private image registry, copy the nf-launcher image to your private registry. Then update your tower.env with the following environment variable:

TOWER_LAUNCH_CONTAINER=<FULL_PATH_TO_YOUR_PRIVATE_IMAGE>

If you're using AWS Batch, you will need to configure a custom job-definition and populate the TOWER_LAUNCH_CONTAINER with the job-definition name instead.