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Seqera Enterprise v25.2

Seqera Platform Enterprise version 25.2 introduces a series of enhancements to improve security, observability, and flexibility.

info

The legacy distribution endpoint at cr.seqera.io/private is deprecated. Only bug fixes for existing major releases will continue to be published there. New major releases of Seqera Platform are available from cr.seqera.io/enterprise. Seqera will provide updated credentials for the new endpoint — contact your Seqera representative if you need access.

Feature updates and improvements​

Single instance cloud compute environments​

Single instance compute environments create a single compute instance to execute Nextflow pipelines or run Studio sessions with a local executor. The new AWS Cloud and Google Cloud compute environments are optimized for small to medium pipelines and Studios, enabling faster startup time, simplified configuration, and fewer cloud provider dependencies. To activate these, add awscloud-platform and googlecloud-platform to the TOWER_ENABLE_PLATFORMS environment variable.

Studios​

Compute changes​
  • Studios now supports ARM64 architecture and Spot instances in AWS Cloud and Google Cloud compute environments.
  • AWS Cloud compute environments now support nested containerization:
    • VS Code Studios include a Docker-in-Docker configuration method, enabling you to run Nextflow directly.
    • The remaining Studios types support Docker via manual installation.
  • Studios now supports path-based routing to enable fixed domains for Studio sessions. This removes the need for a wildcard SSL/TLS certificate.
  • You can now add per-session user-defined environment variables when creating a new Studio.

Data Explorer​

  • Platform CLI now supports file upload and download operations.
  • You can now upload multiple files and folders to your cloud bucket simultaneously.
  • New labels display read-only and public buckets.

Platform interface changes​

  • Replaced the Platform top navigation with a sidebar for improved navigation.
  • The pipeline run details page was refreshed with these improvements:
    • A progress bar provides a clear, dynamic view of pipeline execution in real time.
    • A dedicated Run info tab with a centralized view of run metadata and status details.
    • Improved navigation tabs for Tasks, Logs, Metrics, and Containers.
    • The Tasks tab is the default display for successful runs.

Fusion​

  • Added Fusion Snapshots (beta) support in AWS Batch compute environments, enabling Fusion to automatically restore jobs interrupted by AWS Spot instance reclamation. See Fusion Snapshots for more information.
  • Fusion licensing enabled. A Fusion license sets a specific quota for Fusion use, measured by total pipeline throughput per month (defined by Nextflow's I/O metrics). See Fusion licensing for more information.
  • Added a Platform Fusion usage dashboard.

Audit logs​

  • GxP compliance: Expanded audit log events.
  • Supported IPv6 addresses in audit log UI and API.
  • Audit log API improvements:
    • Pagination improvements for enhanced performance. If you use the audit log admin API in your internal processes, contact us to mitigate any breaking changes to your script.
    • Time range filtering support.

General​

Studios​

  • Added Conda helper text to the Conda packages field in Add new Studio > General config.

Datasets​

  • Added AuditLog for dataset operations.
  • Implemented support for multiple extension dataset parameters in the input form.
  • Datasets with the same name can be stored within the same organization.
  • Renamed data_set_ prefixed events to dataset_ for consistency with Dataset naming.

Launchpad​

  • Added support for providing launch form values via URL query parameters.
  • Added support for markdown rendering for Nextflow object field help_text and description properties.
  • Improved pipeline schema validation error messaging in launch form.
  • Added support for array type parameters in the Launch form.

Workflows​

  • Added Aborted task counts to run details.
  • Updated on-hover copy for Metrics tab data widgets.

Pipelines​

  • Pipeline revision form field formatting in Platform interface.
  • Enabled revision control during fresh pipeline launch.

Compute environments​

  • Upgraded Azure Batch Ubuntu image version to 22.04.
  • Upgraded AWS SDK dependencies to v2.
  • Renamed Pipeline work directory to Work directory in compute environment forms.
  • Added P5, P5e, P6-b200, I7i, C8gd, M8gd and R8gd EC2 families that support NVMe disk. Learn more on the AWS What's New page.

Data Explorer​

  • Added a confirmation dialogue to prevent accidental termination of uploads and downloads by navigating away from Data Explorer.

API​

  • Added OpenAPI tags to endpoints.
  • Added indexes to improve performance on some potentially slow queries.

Bug fixes​

Pipelines​

  • Fixed pipeline secrets not being deleted in the context of a personal workspace.
  • Fixed an issue when editing a pipeline, the logo changed to the organization logo.

Workflows​

  • Fixed missing notifications on tasks in Submitted state.
  • Fixed cost reporting metrics failing to render for runs launched with Nextflow CLI.
  • Fixed empty state condition for containers in the task details screen when using a version of Nextflow that didn't have containerMeta support.
  • Fixed discrepancy between Wall time and total run duration.

Datasets​

  • Fixed content mime types causing overly restrictive dataset parameters.

Data Explorer​

  • Added support for the ? character in Data Explorer path and file names.

Launchpad​

  • Improved launch parameters handling after pipeline revision or config profiles are changed. Revision or config profile changes now override existing parameters.
  • Fixed an issue where parameters did not update on relaunch and removed/modified parameters persisted.

Compute environments​

  • Resolved Google VM propagate instance creation errors.

UI/UX​

  • Updated navigation bar link to Dashboard instead of Launchpad.
  • Improved error message handling for requests that have RequestOptions.responseType explicitly specified.

Nextflow​

Nextflow upgraded to 25.04.3​

Seqera Platform 25.2 includes Nextflow 25.04.3 (previously 24.10.4).

According to the 25.04.0 through 25.04.3 release notes, this is a major update with new features and some breaking changes. 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)
  • Type annotations: Support for type annotations on parameters, workflows, processes, and functions (requires strict syntax)
  • Simpler syntax: Workflow handlers and dynamic directives no longer require closures with strict syntax enabled

Breaking changes:

  • 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 25.04 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=24.10.4

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.

General warnings​

Removed maxSpotattempts setting from Platform​

Nextflow now handles this setting. See the Nextflow reference documentation for more information.

Legacy Seqera container image registry access ended June 1, 2025​

You can no longer pull Seqera Enterprise container images from the legacy Seqera container registries (AWS ECR, GCP AR, Azure CR). All Seqera Enterprise images must be retrieved via the cr.seqera.io container registry. The installation and configuration templates provided for both Docker Compose and Kubernetes installations already reference the cr.seqera.io container image URLs. If you have not yet transitioned to this registry, contact Support to request credentials and for any further assistance.

See Legacy Seqera container image registries for more information on the deprecated Seqera AWS ECR registry.

Upgrade steps​

note
  • Make a backup of your Platform database prior to upgrade.
  • If you are upgrading from a version prior to 25.1, complete all intermediate major version upgrades before upgrading to 25.2.
  • Ensure that no pipelines are in a running state during this upgrade as active run data may be lost.

See Upgrade deployment for installation guidance.

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