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Seqera Cloud v24.2.0_cycle20

Feature updates and improvements​

UI/UX​

  • Added code blocks syntax highlighting and background color.
  • Role selector dropdown detail.
  • Updated navbar help and support links.

Bug fixes​

Launch form​

  • Disabled launch form submit button during form validation.
  • Parameters merging in schema form without key in schema.

Data Studios​

  • Data Studios template override.

Data Explorer​

  • Data Explorer search bar misalignment.

General​

  • Updated team guest welcome email visuals and copy.
  • Tag search with underscore.
  • Added missing gap between shared badge and labels.
  • View credentials back navigation.

Version bumps​

  • Bumped nf-launcher:24.04.3

Wave v1.10.0

Feature updates and improvements​

Container building​

Performance​

General​

Full changelog: https://github.com/seqeralabs/wave/compare/v1.9.0...v1.10.0

Seqera Enterprise v23.4.5

Feature updates and improvements​

General​

  • The standard email login can be disabled via tower.yml or an environment variable, provided an alternative OIDC provider is set up first.

Wave v1.9.0

Feature updates and improvements​

Container building​

Spack​

API​

Performance​

General​

Bug fixes​

Performance​

General​

New Contributors​

Full changelog: https://github.com/seqeralabs/wave/compare/v1.8.2...v1.9.0

Seqera Enterprise v24.1

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 are included in this major release.

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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​

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 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 (GA) 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: Open a connection to a running data studio session and interact with the contents.
  • Maintain: Create, update, start, stop, configure, and delete data studio sessions.
  • View: List, search, and view the status, configuration, and details of data studios.
  • Launch: Open a connection to a running data studio 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 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:

PreviousNew
micronaut.security.token.jwt.generator.access-token.expirationmicronaut.security.token.generator.access-token.expiration

Enterprise deployments that have customized this value previously will need to adopt the new format.

Upgrade steps​

  1. 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.
  2. This version requires a database schema update. Make a backup of your Platform database prior to upgrade.
  3. 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 with the steps below.
  4. 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
  5. See Upgrade installation for database backup and installation upgrade guidance.
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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.

Seqera Enterprise v24.1.1

Feature updates and improvements​

Data Studios​

  • Added the ability to rename data studio checkpoints.

Data Explorer​

  • Added OpenAPI support for Data Explorer.
  • Show loading in Workflow/Task Data Explorer tab while waiting for data link cache refresh.

General​

  • Datasets can now be used in personal workspaces.
  • Pipeline secrets can now be used in personal workspaces.

Compute environments​

  • Added Graviton3 EC2 instance family as valid NVMe instance types.
  • Added new G6 EC2 instance family as valid NVMe instance types.
  • Deprecated EBS autoscale in the Seqera Platform user interface.

Workflows​

  • Retrieve reports from primary compute environment on NF CLI runs.
  • At nf-launcher, propagate a curl failures and exit.

Security updates​

Infrastructure​

  • Upgraded base Docker images to get upstream updates.

Version bump​

Infrastructure​

  • Bumped nf-launcher:j17-23.10.1-up1