Seqera Enterprise v24.2.3
Bug fixes
- Solves an issue with Git URLs in Azure DevOps.
- Bumps Nextflow launcher to 24.10.4.
main.nf
file.Seqera Enterprise version 24.2 introduces new Data Studios features, global Nextflow configuration at the compute environment level, Azure service principal and managed identity authentication support, and a number of bug fixes and performance enhancements.
data_studio_session_build_started
and data_studio_session_build_failed
are added to the audit log events table.workflow/launch
API endpoint. This allows you to specify a custom container using the launchContainer
key in your request body when submitting a workflow execution. For example:
{
"launch": {
"id": "T3xxxxxxxxxxig",
"launchContainer": "quay.io/seqeralabs/nf-launcher:j17-23.10.1-up1",
"computeEnvId": "6Uxxxxxxxxxxxhl",
"workDir": "s3://your-bucket",
"pipeline": "https://github.com/nextflow-io/hello",
...
}
}
al2023-
.ECS_CONTAINER_CREATE_TIMEOUT=10m
: Timeout for creating a container.ECS_CONTAINER_STOP_TIMEOUT=10m
: Timeout for stopping a container. Increase to prevent Nextflow from being forcibly killed and leave running jobs.ECS_MANIFEST_PULL_TIMEOUT=10m
: Timeout for pulling a container manifest. This may be needed when pulling a Wave container with a long build time.This requires a change to pipeline configurations that previously used Spot auto-retry for AWS and Google Cloud Batch.
$TW_AGENT_WORKDIR
as working directory.javax.mail
transitive dependency problem.managedIdentityId
to the API response payload when describing a compute environment.quicklaunchmode
, even if revision is empty.tw_workflow(complete)
column, which improves the performance of the query that finds workflows with missing progress. Added an index to the tw_workflow(status)
column conditionally; the index was already present in the cloud.seqera.io
database, but not previously included in the database migration scripts.lastUsed
on compute environment when creating a job for a Data Studios session.TOWER_CONTENT_URL
set.From this version of Seqera Platform, redisson.*
configuration properties are deprecated. If you have set redisson.*
properties directly previously, do the following:
/redisson/*
references in AWS Parameter Store entries with TOWER_REDIS_*
.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 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.
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'
The property that determines the expiration time of the JWT access token (used for authenticating web sessions and Nextflow-Platform interactions) has changed since 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.
Upgrading to version 24.2 requires backend downtime in order for the database migration to complete successfully.
running
state as active run data may be lost.tower.env
, configmap.yml
, etc.):
JAVA_OPTS: -Xms1000M -Xmx2000M -XX:MaxDirectMemorySize=800m -Dio.netty.maxDirectMemory=0 -Djdk.nio.maxCachedBufferSize=262144
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 24.2 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.
determineTextFormat
helper function.tower.yml
or an environment variable, provided an alternative OIDC provider is set up first.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.
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.
Data Studios is available as a public preview. Contact support to request access to this feature.
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.
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:
See User roles for more information.
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.
tower.yml
or an environment variable, provided an alternative OIDC provider is set up first. See Basic configuration for more information.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:
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.
running
state as active run data may be lost.tower.env
, configmap.yml
, etc.):
JAVA_OPTS: -Xms1000M -Xmx2000M -XX:MaxDirectMemorySize=800m -Dio.netty.maxDirectMemory=0 -Djdk.nio.maxCachedBufferSize=262144
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.