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Seqera Enterprise v25.3.4

Feature updates and improvements​

Compute environments​

  • Added support for ${username} dynamic notation in resource labels.

Studios​

  • Added configurable SSH timeout parameters for Studios connections.

Pipelines​

  • Improved workflow status transitions so that workflows in an unknown state correctly transition to running when a begin trace is received.
  • Updated schema radio control labels for clarity.

Bug fixes​

Compute environments​

  • Fixed an issue where resourceLabelIds was incorrectly tracked as a versionable compute environment control.

Pipelines​

  • Fixed job scheduler transaction rollback handling to prevent data inconsistency when an exception occurs while saving job status.
  • Fixed implicit default version resolution for pipelines.

Platform API​

  • Fixed Task.getExit() return type alignment to Integer in the API.

Monitoring and observability​

  • Fixed cookie banner visibility logic for enterprise deployments to correctly hide the banner when no non-essential cookies are configured.

Upgrade notes​

No breaking changes. Standard upgrade procedure applies.

Seqera Enterprise v25.3.3

Feature updates and improvements​

Studios​

  • (Public preview) Added SSH connectivity to Studios which enables direct connection to running Studio sessions using standard SSH clients, supporting VS Code Remote SSH and terminal access. See Studios SSH configuration for more information.

Pipelines​

  • Added custom schema support to pipeline versions.
  • Added edit launch pipeline.
  • Enabled custom schema retrieval for pipeline versions.

See Pipeline versioning for more information.

Access Control​

  • Removed participants on workspace deletion.
  • Improved error message when deleting custom roles.
  • Added pagination to roles list page.
  • Added the ability to view an effective permissions summary for any user/workspace combination in the UI or via API.
  • Added the ability to reset a custom role's permissions to match any predefined role (Admin, Maintain, Launch, Connect, View).

Custom roles quota enforcement​

The maxCustomRolesPerOrg quota is now enforced on custom role creation. Organizations at or near their quota limit will be unable to create additional custom roles. Review your organization's custom role usage if you need to create additional roles. Contact support to adjust your quotas if needed.

General​

  • Restored custom navigation menu support in user dropdown.
  • Updated styles for container responsiveness and padding adjustments and footer.
  • Added only current page in task pagination.
  • Added storage for SSH public keys for use in Studios.

Bug fixes​

  • Cleared parameters when changing between pipeline with and without parameters.
  • Fixed correctly updated versions list when version is published.
  • Prevented re-assignations of pipeline.launch when working with versions.
  • Updated schema when schemaName field value changes.
  • Prevented adding empty parameters when reseting parameters form with defaults after config profile change.

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 or Studio sessions are in a running state during this upgrade as active run data and analysis may be lost.

See Upgrade deployment for installation guidance.

Seqera Enterprise v25.3.1

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.

Seqera Enterprise v25.3

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.

Feature updates 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.

General​

  • 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 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​

Studios​

  • Fixed Studios AWS cloud private ECR pull issues.
  • Fixed handling of Studios tokens without user ID claim.
  • Fixed trigger YAML validation on Studios config patch.

Pipelines​

  • Fixed pipeline list not updating when changing workspace.
  • Fixed pipeline config reading from same directory as main script.
  • Fixed describePipeline to properly handle avatar files.

Workflows​

  • Prevented incorrect workdir patching when resuming workflow with compute environment changes.
  • Added proper permission checks for workflow star functionality.

Compute environments​

  • Fixed transactional event listener annotation for compute operations.
  • Improved Connect parameter handling for compute environments.
  • Fixed error when saving long container names.

UI/UX​

  • Fixed MultiQC plots displaying as grey boxes.
  • Fixed badge cropping issues in Platform UI.
  • Fixed infinite scroll in optimization profile modal.
  • Forced perfect circle avatar shape for consistent rendering.

Permissions and roles​

  • Removed blanket ListOrganizationSettings check, use individual permissions instead.

General​

  • Fixed OIDC API handling in authentication flows.

Fusion​

See the Fusion changelog for more details.

Wave​

See the Wave changelog for more details.

Nextflow​

Nextflow upgraded to 25.04.8​

Seqera Platform 25.3 includes Nextflow 25.04.8 (previously 25.04.3 from v25.2).

According to the 25.04.0 through 25.04.8 release notes, this update includes bug fixes and stability improvements. Existing pipelines will continue to work.

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=25.04.x

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.

MultiQC​

See the MultiQC changelog for details.

General warnings​

Starting in version 26.1, the root user image is deprecated. We recommend switching to the unprivileged (rootless) image during this upgrade. To do so:

  • Update the image tag.
  • Modify your Kubernetes Service resource or Docker Compose service definition to forward requests to port 8000 (the default for the unprivileged image).

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

Feature updates 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.

Workflows​

  • 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.
  • The progress response now includes retries and ignored status task counts when a workflow is finalized.

Pipelines​

  • 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​

Pipelines​

  • 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.