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Changelog

Seqera Cloud v25.1.0_cycle9

Seqera Cloud

Feature updates and improvements​

  • Fusion
    • Add Fusion Snapshots support in AWS Batch compute environments, enabling Fusion to automatically restore jobs interrupted by AWS Spot instance reclamation. See Fusion Snapshots for more information.

Bug fixes​

  • Fix container table pagination.
  • Make task-level containers tab visible only when containers are available.
  • Fix a launch form issue with eager parameter keyword interpolation.

Seqera Cloud v25.1.0_cycle7

Seqera Cloud

Feature updates and improvements​

  • Data Explorer
    • You can now drag and drop multiple folders or files to upload them to your cloud bucket, or you can select Upload, then select multiple files to upload.
  • Fusion:
    • The Seqera-optimized AMI is now the default for the single VM compute environment. If no AMI is specified when adding a compute environment, it defaults to the Seqera-optimized AMI.
  • Add a more detailed warning for workflow cleanup issues that are related to access restrictions to the AWS Batch compute environment.
  • Add support for array type parameters in the Launch form.
  • Implement support for multiple extension dataset parameters in the input form.
  • Delete pipeline secrets in the user context from the provider.
  • Switch logs, secrets-manager, marketplace-meter, and simple-email dependencies to AWS SDK v2.
  • Show Nextflow config parameters that are binary expressions in the Launch form.
  • Add azure_entra to the provider list of credentials in the OpenAPI spec.
  • Switch AWS S3 to SDK v2.
  • Add task status badges with icons to the workflow run tasks table.

Bug fixes​

  • Modify cache expiration policy to resolve "Connection pool shut down" error with new AWS SDK v2 clients.
  • Fix an issue where the workflow details page displays the Edit Labels button even when there are no labels, but resource labels are attached to the workflow.
  • Fix an issue where the Quick Launch form did not select the primary compute environment by default.

Seqera Enterprise v24.2.5

Seqera Enterprise

General​

This release backports the default Azure image fix from v25.1.1 to v24.2.x:

Azure Batch support for Ubuntu 20.04 LTS ending

The default Azure Batch Ubuntu image has been updated with sku 22.04. This is to ensure there are no issues with the existing Azure Batch Ubuntu image (sku 20.04) which will be deprecated after April 23, 2025. See, https://github.com/Azure/Batch/issues/174 for more information about the deprecation.

Seqera Enterprise v25.1.1

Seqera Enterprise

General​

  • Azure Batch support for Ubuntu 20.04 LTS ending: The default Azure Batch Ubuntu image has been updated with sku 22.04. This is to ensure there are no issues with the existing Azure Batch Ubuntu image (sku 20.04) which will be deprecated after April 23, 2025. See, https://github.com/Azure/Batch/issues/174 for more information about the deprecation.
  • Implement support for multiple extension dataset parameters in the input form.

Seqera Enterprise v25.1

Seqera Enterprise

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.

New features 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 attached 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.
  • Add support for Fusion licensing.

General​

  • Updated list of EC2 families with NVMe disks available.
  • Audit log update: Pipeline edit events are now logged.
  • Switch AWS Batch compute environment dependencies to AWS SDK v2.
  • Switch Compute dependencies to AWS SDK v2.
  • 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:
    1. A valid icon key:value pair defined in the manifest object of the nextflow.config file.
    2. The GitHub organization avatar (if the repository is hosted on GitHub).
    3. If none of the above are defined, Platform auto-generates and attaches a pipeline icon.
  • New dynamic page title for easy bookmarking.
  • Added totalProcesses to workflow progress responses.
  • Implement collapsible view for JSON workflow parameters tab and add View as YAML option.
  • Update the pipeline name regular expression to allow pipeline names containing dots ('.').
  • Allow Nextflow configuration parameters with embedded references to other parameters to be shown verbatim.
  • 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.
  • Azure jobs are now automatically terminated after all tasks are complete.
  • Send only added/updated run parameters when launching a pipeline. This includes all defaults and parameters passed during the launch.
  • Allow users to remove organization logos.
  • New workflow job monitoring collects and publishes Platform metrics.
  • Notify the user when secrets cleanup fails.
  • Dashboard page: Add a date filter.
  • Bump nf-launcher default to version 25.10.5.
  • Upgrade to Angular 18.

Bug fixes​

  • Studios
    • Fixed resource labels being erroneously non-editable for the Maintain role when adding or starting a Studio session.
    • Fixed searches for names containing special SQL wildcard characters (_, %).
  • 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.
  • 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.
  • Disable reset selection on data change in workflow list component.
  • Take into account the alternative mainScript path.
  • Use preferred_username as fallback email field for OIDC login.
  • Drop the last characters in job definition names longer than the prescribed limit.
  • Fixed an additional reference to the mainScript parameter in the pipeline-info API response.
  • Fixed a problem with Entra and javax.mail transitive dependency.
  • 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.
  • 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.

Breaking changes and warnings​

OIDC Secrets injection modifications​

The auth-oidc-secrets Micronaut environment has been replaced with oidc-token-import. 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:

  • Replace /redisson/* references in AWS Parameter Store entries with TOWER_REDIS_*.
  • Replace redisson.* references in tower.yml with TOWER_REDIS_*.
note

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:

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​

warning

Upgrading to version 25.1 requires backend downtime in order for the database migration to complete successfully.

  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 25.1 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 installation upgrade guidance.
info

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.

Wave v1.19.4

Wave

Feature updates and improvements​

  • Add enable-native-access=ALL-UNNAMED to launch options by @pditommaso in 4f0525da
  • Convert default request containerPlatform to linux/adm64 by @pditommaso dcdb7cf4
  • Fix NPE accessing job manager config by @pditommaso in #812
  • Normalize arch argument to platform by @pditommaso in f2a3db7b
  • Remove unused platform variable by @pditommaso in 77bbb416
  • Revert use of async Caffeine cache by @pditommaso in #811
  • Use uniform notation for resources requests & limits by @pditommaso in #819
  • Bump nf-jdk:corretto-24-al2023-jemalloc by @pditommaso in bcb14150

Full changelog: https://github.com/seqeralabs/wave/compare/v1.19.3...v1.19.4