Enterprise 24.1.x

In order to ensure our customers have success with Seqera Platform 24.1+ we recommend pausing planned upgrades to 24.1+ on production systems until further notice.

Our team has identified an issue in a dependency library which may cause a memory leak under certain conditions at scale. While we have not seen this issue surface in any production Enterprise deployments, we recommend pausing release plans while we work on expediting a fix with the library maintainers.

We have reached out to all users running 24.1 directly and recommend continuing Seqera Platform use as normal while waiting for a patch release.

If you have any further questions, please contact support.

Seqera Platform Enterprise version 24.1 introduces three new features: Data Studios (in public preview), Data Explorer, and managed identities. A number of bug fixes and performance enhancements have also been included in this major release.

Data Studios

Data Studios closes the loop from development to deployment and insights, allowing you to create, manage, and share notebook environments in Seqera with the click of a button. Data Studios also makes it seamless to work across teams with multi-user support, built-in authentication, and automatic snapshots as you work.

• Host a combination of container images and compute environments for interactive analysis using your preferred tools, like Jupyter notebooks, RStudio, and Visual Studio Code IDEs.
• Checkpoints provide a stable point-in-time snapshot.
• Collaborate and share data in real time.

Data Studios is available as a public preview. Contact support to request access to this feature.

Data Explorer

Data Explorer allows you to browse and interact with remote data repositories from organization workspaces in Seqera Platform. It supports AWS S3, Azure Blob Storage, and Google Cloud Storage repositories.

Data Explorer is now Generally Available and supports multi-file and multi-folder download. This allows users to download entire datasets of pipeline results to share with their team.

Extended data roles

User roles provide flexibility for admins to provide users with the permissions they need, without compromising security. The Connect user role has been added to the existing user roles with functionality related to Data Studios:

• Connect: The ability to open a connection to a running session and interact with the contents.
• Maintain: The ability to create, update, start, stop, change configuration, and delete data studio sessions.
• View: The ability to list, search, and see the status/configuration/details of data studios.
• Launch: The ability to open a connection to a running session and interact with the contents.

See User roles for more information.

Managed identities

Managed identities offer significant advantages for High-Performance Computing (HPC) environments by enabling granular access control for individual workspace users. Unlike traditional SSH credentials that grant all workspace users access to HPC clusters with the same service account, managed identities ensure each user’s activity is logged under their own credentials.

See Managed identities for more information.

Other feature improvements

• A redesigned pipeline launch form provides an improved workflow and an interface to create and edit run parameters as raw JSON/YAML. Enable the new launch form per workspace via environment variable.
• Retrieve reports from primary compute environment on Nextflow CLI runs. See Configure reports for Nextflow CLI runs for more information.
• The standard email login can be disabled via tower.yml or an environment variable, provided an alternative OIDC provider is set up first. See Basic configuration for more information.

Breaking changes

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) should be updated accordingly when upgrading to Platform version 24.1.1 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:

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

In order to ensure our customers have success with Seqera Platform 24.1+ we recommend pausing planned upgrades to 24.1+ on production systems until further notice.

Our team has identified an issue in a dependency library which may cause a memory leak under certain conditions at scale. While we have not seen this issue surface in any production Enterprise deployments, we recommend pausing release plans while we work on expediting a fix with the library maintainers.

We have reached out to all users running 24.1 directly and recommend continuing Seqera Platform use as normal while waiting for a patch release.

If you have any further questions, please contact support.

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 24.1.1 with the steps below.

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 24.1 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.

Follow these steps to update your DB instance and the Seqera installation:

The database volume is persistent on the local machine by default if you use the volumes key in the db or redis section of your docker-compose.yml file to specify a local path to the DB or Redis instance. If your database is not persistent, you must back up your database before performing any application or database upgrades.

1. Make a backup of the Seqera Platform database. If you use the pipeline optimization service and your groundswell database resides in a database instance separate from your Seqera database, make a backup of your groundswell database as well.
2. Download the 24.1 versions of your deployment templates and update your Seqera container versions:
   • docker-compose.yml for Docker Compose deployments
   • tower-cron.yml and tower-svc.yml for Kubernetes deployments
3. Restart the application.
4. If you're using a containerized database as part of your implementation:
   1. Stop the application.
   2. Upgrade the MySQL image.
   3. Restart the application.
5. If you're using Amazon RDS or other managed database services:
   1. Stop the application.
   2. Upgrade your database instance.
   3. Restart the application.
6. If you're using the pipeline optimization service (groundswell database) in a database separate from your Seqera database, update the MySQL image for your groundswell database instance while the application is down (during step 4 or 5 above). If you're using the same database instance for both, the groundswell update will happen automatically during the Seqera database update.

Custom deployment:

• Run the /migrate-db.sh script provided in the migrate-db container. This will migrate the database schema.
• Deploy Seqera following your usual procedures.

Nextflow launcher image

If you must 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 launch container 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.

Changelog

For a detailed list of all changes, see the Seqera changelog.