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Changelog: Seqera Enterprise

Seqera Enterprise v25.3

Seqera Enterprise

Seqera Platform Enterprise version 25.3 introduces a series of new features and enhancements, including custom user roles, Studios integration with Git providers, and pipeline versioning.

New features and improvements​

Custom roles and fine-grained authorization (RBAC)​

  • Added support for custom roles with fine-grained permissions, to define specific access controls beyond the predefined Owner, Admin, Maintain, Launch, View, and Connect roles.

Studios​

  • Updated the Add Studio page to a single-step form.
  • Added support for Azure single VM compute environments.
  • Added support for loading Studio configuration from private and public Git repositories.
  • Added ability to clone content from a Git repository to a Studio at startup time.
  • Added ability to create Studios from Docker images, built from a repository Dockerfile using Wave.
  • Added ability to stop a Studio session that is stuck starting without needing AWS console access.
  • Added Save as data link action when mounting data to a Studio.
  • Added support for custom environment variables to Studio configuration.

Pipelines​

Datasets​

  • Refactored datasets list and detail views with additional metadata and improved version control.
    • Added ability to dynamically show/hide datasets for all users in the workspace. Hidden datasets do not consume workspace quota.
    • Removed dataset quota limits.
    • Added ability to sort dataset list by name, recently updated, and recently used.
    • Added support for labels.
    • Enhanced filtering of all dataset attributes (visibility, label, username, createdAfter, createdBefore, updatedAfter, updatedBefore, usedAfter, usedBefore).
    • Added one-click view of all pipeline runs using a specific dataset, adding direct traceability between datasets and workflow runs.

Data Explorer​

  • Added support for S3-compatible object storage providers. To use additional object storage providers, update the unprivileged CSP policy.
  • Added support for LakeFS Cloud in Data Explorer by enabling image preview and file upload functionality when using LakeFS Cloud as an S3-compatible storage provider.
  • Added CSP config for OCI Object Storage, Cloudflare R2, and LakeFS Cloud.

Compute​

  • Configured Nextflow to automatically terminate unschedulable jobs on AWS Batch compute environments by setting aws.batch.terminateUnschedulableJobs to true by default. This prevents jobs that cannot be scheduled (due to invalid resource requests or configuration errors) from indefinitely blocking the job queue.
  • Implemented safeguards to prevent unschedulable jobs from blocking other jobs in the queue. When jobs cannot be scheduled due to resource constraints or configuration errors, they are handled separately to ensure other valid jobs can proceed.
  • Added the AWS g6e instance family (NVIDIA L40S GPUs) to the NVMe disk support list, enabling high-performance instance storage for GPU-accelerated workloads.
  • Added f2.6xlarge, f2.12xlarge, f2.48xlarge instance types.
  • Extended Google Cloud config with selectable Advanced options - machineType, image, armEnabled.

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​

  • Bumped Nextflow launcher to nf-launcher:j21-25.04.8.
  • Replaced the top navigation with a sidebar in Platform.
  • Updated Platform behavior to redirect to first available sidenav item instead of hardcoded launchpad.
  • Added usage statistics to the Datasets API, allowing you to view the number of pipeline runs using each dataset and when it was last used.
  • Added metrics to confirm whether a pipeline is running GPU resources.
  • Added better support for treating Nextflow config preferentially, as mono-repo configurations are now read from the same directory as the configured main script.
  • Added support for BitBucket API tokens to ensure that Bitbucket can still be used as an API provider. See the announcement for more information: https://bitbucket.org/account/settings/app-passwords/.

Bug fixes​

  • Fixed Studios AWS cloud private ECR pull issues.
  • Fixed handling of Studios tokens without user ID claim.
  • Fixed MultiQC plots displaying as grey boxes.
  • Fixed badge cropping issues in Platform UI.
  • Fixed infinite scroll in optimization profile modal.
  • Removed blanket ListOrganizationSettings check, use individual permissions instead.
  • Added proper permission checks for workflow star functionality.
  • Forced perfect circle avatar shape for consistent rendering.
  • Fixed pipeline list not updating when changing workspace.
  • Prevented incorrect workdir patching when resuming workflow with compute environment changes.
  • Fixed pipeline config reading from same directory as main script.
  • Fixed error when saving long container names.
  • Fixed trigger YAML validation on Studios config patch.
  • Fixed describePipeline to properly handle avatar files.
  • Fixed transactional event listener annotation for compute operations.
  • Improved Connect parameter handling for compute environments.
  • Fixed OIDC API handling in authentication flows.

Fusion​

See the Fusion changelog for more details.

Wave​

See the Wave changelog for more details.

Nextflow​

See the Nextflow migration notes page for changelog details.

MultiQC​

See the MultiQC changelog for details.

General warnings​

Starting from version 26.1, the front end image running as root user will be deprecated. We recommend starting to switch to the root-less image (also known as "unprivileged" image) during this upgrade. See Kubernetes and docker-compose deployment documentation for instructions.

Upgrade steps​

This release maintains backward compatibility with version 25.2.x.

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 25.3.
  • 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.

Seqera Enterprise v25.2.3

Seqera Enterprise

New features and improvements​

  • Studios
    • Added three new configuration parameters for customizing Docker image naming conventions in Studios Wave integration.
    • Added eStarGZ support for Studios with conda packages.
  • Platform
    • Introduced multiple improvements to the Usage Overview to simplify compute usage tracking.
    • Added automatic memory tracking for billing to automatically capture actual memory usage for tasks without explicit memory limits, ensuring accurate consumption tracking.
  • Pipelines
    • retries and ignored status task counts are now included in progress response when a workflow is finalized.
    • Improved loading time for pipeline details (up to 700ms improvement) for repositories like nf-core/rnaseq. This resolves timeout issues when launching pipelines.

Bug fixes​

  • Fixed a missing newline in the includeCustomUserConfig method and resolved an issue where where custom config includeConfig statements were improperly concatenated, causing syntax errors when parsed.

Seqera Enterprise v25.2

Seqera Enterprise

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

New features 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.
  • Nested containerization is now supported in AWS Cloud compute environments:
    • 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​

  • The Platform top navigation has been replaced with a sidebar for improved navigation.
  • The pipeline run details page has been refreshed and includes 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 now the default 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.
  • Enabled Fusion licensing. 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.
  • Support for 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​

  • Bumped Nextflow launcher to 25.04.x.
  • Added Conda helper text to the Conda packages field in Add new Studio > General config.
  • Added AuditLog for dataset operations.
  • 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.
  • Added Aborted task counts to run details.
  • Pipeline revision form field formatting in Platform interface.
  • Improved pipeline schema validation error messaging in launch form.
  • Upgraded Azure Batch Ubuntu image version to 22.04.
  • Upgraded AWS SDK dependencies to v2.
  • Added support for array type parameters in the Launch form.
  • Implemented support for multiple extension dataset parameters in the input form.
  • Renamed Pipeline work directory to Work directory in compute environment forms.
  • Updated on-hover copy for Metrics tab data widgets.
  • Added a confirmation dialogue to prevent accidental termination of uploads and downloads by navigating away from Data Explorer.
  • Datasets with the same name can be stored within the same organization.
  • 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.
  • Renamed data_set_ prefixed events to dataset_ for consistency with Dataset naming.
  • Added indexes to improve performance on some potentially slow queries.
  • Added OpenAPI tags to endpoints.
  • Enabled revision control during fresh pipeline launch.

Bug fixes​

  • Fixed pipeline secrets not being deleted in the context of a personal workspace.
  • Fixed missing notifications on tasks in Submitted state.
  • Fixed content mime types causing overly restrictive dataset parameters.
  • Fixed cost reporting metrics failing to render for runs launched with Nextflow CLI.
  • Updated navigation bar link to Dashboard instead of Launchpad.
  • Fixed empty state condition for containers in the task details screen when using a version of Nextflow that didn’t have containerMeta support.
  • Added support for the ? character in Data Explorer path and file names.
  • Improvement to launch parameters handling after pipeline revision or config profiles are changed. Existing parameters are now overridden during a revision or config profile change.
  • Fixed an issue where parameters were not updating on relaunch and removed/modified parameters were persisting.
  • Improved error message handling for requests that have RequestOptions.responseType explicitly specified.
  • Fixed discrepancy between Wall time and total run duration.
  • Fixed an issue when editing a pipeline, the logo changed to the organization logo.
  • Resolved Google VM propagate instance creation errors.

General warnings​

Removed maxSpotattempts setting from Platform​

This setting is now handled by Nextflow. 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.