Seqera Platform Enterprise version 25.1 introduces Studios GA and a number of bug fixes and performance enhancements.
Studios is Seqera's in-platform tool for secure, on-demand, interactive data analysis using containers created from Seqera-managed container template images or your own organization-managed custom environments. You only pay for the compute your Studio sessions consume, and the compute is adjacent to your data, significantly reducing data transfer costs and wasted time copying data from storage to analysis. This significantly reduces infrastructure management requirements, removes data silos, adheres to strict in-platform role-based access control, and lowers your operational costs. Learn more about Studios.
Feature updates and improvements
Studios
- Labeled templates: Labels indicate the status of support (
recommended or deprecated) for a Seqera-managed Studio container template version. Users can migrate a Studio to a new base container template when Adding as new.
- Private sessions: When adding a new Studio, the number of concurrent connections (private vs. all workspace members) can now be defined in General Config > Collaboration.
- Custom session lifespans: This new feature allows you to set a maximum lifespan for a session, after which time the session is stopped automatically and a checkpoint created, or the session can be extended on-demand.
- Resource labels: Users with at least workspace maintainer role permissions can manage the resource labels inherited from the compute environment and attach them to the Studio. Resource labels attached to each Studio don't affect the default resource labels associated with the compute environment.
Fusion
- AWS Batch compute environments default to Amazon Linux 2023 AMI when Fusion v2 is enabled.
- Added support for Fusion licensing.
General
Compute environments
- Updated list of EC2 families with NVMe disks available.
- Switch AWS Batch compute environment dependencies to AWS SDK v2.
- Switch Compute dependencies to AWS SDK v2.
- Platform now automatically terminates Azure jobs after all tasks are complete.
Audit logs
- Audit log update: Pipeline edit events now logged.
Pipelines
- You can upload custom icons when adding or updating a pipeline. If no user-uploaded icon is defined, Platform will retrieve and attach a pipeline icon in the following order of precedence:
- A valid
icon key:value pair defined in the manifest object of the nextflow.config file.
- The GitHub organization avatar (if the repository is hosted on GitHub).
- If none of the above are defined, Platform auto-generates and attaches a pipeline icon.
- Updated the pipeline name regular expression to allow pipeline names containing dots ('.').
- Improved error messaging when pipeline information can't be fetched indicates whether the issue is due to a missing resource, or failed authentication due to expired credentials.
Workflows
- Added
totalProcesses to workflow progress responses.
- New workflow job monitoring collects and publishes Platform metrics.
- Notify the user when secrets cleanup fails.
Launchpad
- Implemented collapsible view for JSON workflow parameters tab and add View as YAML option.
- Allow Nextflow configuration parameters with embedded references to other parameters to be shown verbatim.
- Send only added/updated run parameters when launching a pipeline. This includes all defaults and parameters passed during the launch.
UI/UX
- New dynamic page title for easy bookmarking.
- Allow users to remove organization logos.
- Dashboard page: Add a date filter.
Bug fixes
Studios
- Fixed resource labels erroneously non-editable for the Maintain role when adding or starting a Studio session.
- Fixed searches for names containing special SQL wildcard characters (_, %).
Credentials
- Prohibit duplicate Git credentials and tie-break on
lastUpdated for existing duplicates. Preference is given to the last-updated credentials when there are multiple candidates. A check is also added to avoid duplicates when creating new credentials.
Compute environments
- Set
ECS_CONTAINER_START_TIMEOUT to 10 minutes in the ECS settings used by AWS Batch CEs, to prevent Task failed to start - DockerTimeoutError: Could not transition to started; timed out after waiting 3m0s errors.
- Compute environment creation form allows pre- and post-run scripts to be longer than the accepted value of 1024 characters.
- Drop the last characters in job definition names longer than the prescribed limit.
- Fallback to primary compute environment when launching a shared pipeline without an associated compute environment from a private workspace.
- Fixed regression of the quick launch form not selecting the primary compute environment by default.
Workflows
- Disabled reset selection on data change in workflow list component.
Pipelines
- Take into account the alternative
mainScript path.
- Fixed an additional reference to the
mainScript parameter in the pipeline-info API response.
- A change in the nf-core tools template made config profile search in the pipeline launch form inconsistent in Platform as it's prepended by a ternary operator. This release introduces a fix that improves config profile name parsing.
- Do not fetch info for
INVALID status pipelines, fetch for all other statuses including DISABLED.
General
- Use
preferred_username as fallback email field for OIDC login.
- Fixed a problem with Entra and
javax.mail transitive dependency.
Nextflow
Nextflow upgraded to 24.10.5
Seqera Platform 25.1 includes Nextflow 24.10.5 (previously 24.10.4 from v24.2).
According to the 24.10.0 through 24.10.5 release notes, this update includes improvements and bug fixes. Existing pipelines will continue to work.
See the Nextflow 24.10 migration guide for full details.
The default Nextflow version can be overridden by setting NXF_VER in a pre-run script:
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.
Breaking changes and warnings
OIDC Secrets injection modifications
oidc-token-import replaces the auth-oidc-secrets Micronaut environment. If you use this configuration, you must change the MICRONAUT_ENV environment variable in the manifest during the migration process. If you activate the feature with the TOWER_OIDC_TOKEN_IMPORT environment variable, no changes are needed.
Seqera AWS ECR repository customer access ends June 1, 2025
Customers will no longer be able to pull Seqera Enterprise container images from the legacy Seqera AWS ECR repository after June 1, 2025. All Seqera Enterprise images must be retrieved via the cr.seqera.io container registry after this cutoff date. 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 AWS ECR and other deprecated Seqera container registries.
Redis version change
From Seqera Enterprise version 24.2:
- Redis version 6.2 or greater is required.
- Redis version 7 is officially supported.
Redisson properties deprecated
From Seqera Enterprise version 24.2, redisson.* configuration properties are deprecated. If you have set redisson.* properties directly previously, do the following:
- Replaced
/redisson/* references in AWS Parameter Store entries with TOWER_REDIS_*.
- Replaced
redisson.* references in tower.yml with TOWER_REDIS_*.
Set TOWER_REDIS_* values directly in the tower.yml or AWS Parameter Store entry (for example, TOWER_REDIS_URL: redis://...).
MariaDB driver: New MySQL connection parameter required
MariaDB driver 3.x requires a special parameter in the connection URL to connect to a MySQL database:
jdbc:mysql://<domain>:<port>/tower?permitMysqlScheme=true
All deployments using a MySQL database (regardless of version: 5.6, 5.7, or 8) must be updated when upgrading to Seqera Enterprise version 24.1 or later.
MariaDB driver: No truncation support for MySQL 5.6
The MariaDB driver has dropped support for the jdbcCompliantTruncation parameter, which was true by default and set the STRICT_TRANS_TABLES SQL mode. The STRICT_TRANS_TABLES mode produces an error when the value of a VARCHAR column exceeds its limit, instead of truncating it to fit. Most common installations of MySQL 5.7 and 8 already include this mode at the server level, but the Docker container version of MySQL 5.6 does not.
The SQL mode must be set explicitly through the connection URL for deployments still using MySQL 5.6:
jdbc:mysql://<domain>:<port>/tower?permitMysqlScheme=true&sessionVariables=sql_mode='STRICT_TRANS_TABLES,NO_ENGINE_SUBSTITUTION'
Micronaut property key changes
The property that determines the expiration time of the JWT access token (used for authenticating web sessions and Nextflow-Platform interactions) has changed as of Seqera Enterprise version 24.1:
| Previous | New |
|---|
micronaut.security.token.jwt.generator.access-token.expiration | micronaut.security.token.generator.access-token.expiration |
Enterprise deployments that have customized this value previously will need to adopt the new format.
Upgrade steps
Upgrading to version 25.1 requires backend downtime in order for the database migration to complete successfully.
- This version includes an update to the Platform Enterprise H8 cache. Do not start the upgrade while any pipelines are in a
running state as active run data may be lost.
- This version requires a database schema update. Make a backup of your Platform database prior to upgrade.
- If you are upgrading from a version older than 23.4.1, update your installation to version 23.4.4 first, before updating to 25.1 with the steps below.
- For recommended Platform memory settings, add the following environment variable to your Platform configuration values (
tower.env, configmap.yml, etc.):
JAVA_OPTS: -Xms1000M -Xmx2000M -XX:MaxDirectMemorySize=800m -Dio.netty.maxDirectMemory=0 -Djdk.nio.maxCachedBufferSize=262144
- See Upgrade installation for installation upgrade guidance.
Docker Compose deployments require downtime while upgrading services. Restarting the application may take several minutes. See Docker compose deployment for more information.
For Kubernetes deployments, apply the 25.1 tower-cron.yml to your cron pod and wait for the cron pod to be running before applying the tower-svc.yml to your backend pod and restarting the service. If the cron pod update is interrupted, you may need to restore the instance from your DB backup and start again. See Kubernetes deployment for more information.
For custom deployments with third-party services such as ArgoCD, contact support for assistance during upgrade.