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Changelog

Wave v1.6.0

Wave

Feature updates and improvements​

Bug fixes​

Full changelog: https://github.com/seqeralabs/wave/compare/v1.5.2...v1.6.0

Wave v1.5.0

Wave

Feature updates and improvements​

Full changelog: https://github.com/seqeralabs/wave/compare/v1.4.0...v1.5.0

Seqera Enterprise v23.4.0

Seqera Enterprise

Breaking changes​

  • Breaking change: Update docker-compose in deployment files to docker compose.
  • Breaking change: SQL migration enhancements for MySQL 5.7 and above (see Upgrade steps.

Feature updates and improvements​

  • Allow previewing of Nextflow output files in Data Explorer.
  • Seqera Platform Enterprise license model change — requires new licenses for existing Enterprise customers.
  • Remove tower.enable.arm64 config option.
  • Changed default AzBatch image to ubuntu-server.
  • Set private address for head job configuration in Google Batch.
  • VM instance template support for Google Batch.

Version bump​

  • Bump nf-jdk:corretto-17.0.10-jemalloc as base image.
  • New base image nginx 1.25.3 for tower-frontend unprivileged.
  • Upgrade Bootstrap to version 5.

Seqera Enterprise v23.4

Seqera Enterprise

Seqera Platform Enterprise version 23.4 introduces a redesigned UI, VM instance template support for Google Cloud Batch, and database deployment improvements. A number of bug fixes and performance enhancements have also been included in this major release.

note

Version 23.4.6 is the baseline for the 23.4 major release cycle.

New features and improvements​

Form redesign​

Seqera Platform 23.4 features refreshed forms and UI elements aimed at enhancing user experience and streamlining form navigation. This redesign encompasses all application interface forms, including pipelines, compute environments, Data Explorer, and administrative pages to create a more intuitive user journey.

Google Cloud Batch: VM instance template support​

Seqera now supports VM instance templates for head and compute jobs in Google Cloud Batch compute environments. VM instance templates provide a convenient way to save a VM configuration, thereby allowing you to define the resources allocated to Batch jobs.

General​

  • Forms UI copy improvements
  • Update docker-compose in deployment files
  • Improved database migration via new migrate-db container
  • Changed default Azure Batch image to ubuntu-server
  • Set private address for head job configuration in Google Batch
  • Nextflow output file preview in Data Explorer

Enterprise licensing update​

Platform Enterprise 23.4 includes an update to the Enterprise licensing model. While Seqera support will contact affected customers to update licenses, the license manager remains backward compatible with existing licenses. For standard Enterprise licenses, no customer action is required. License limits are enforced remotely — if your Enterprise license includes custom limits, contact Seqera support to ensure a seamless transition.

MySQL version in deployment manifests bumped to version 8​

Seqera Platform Enterprise version 23.4 officially supports MySQL 8.0. The default MySQL version in the docker-compose.yml and tower-cron.yml deployment templates for Docker Compose and Kubernetes deployments has been updated from 5.7 to 8.0 in the Seqera version 23.4 documentation. See Upgrade steps below for instructions to update your Seqera databases from older versions to MySQL 8.

Previous versions of the deployment template files are still available in Platform docs versions 23.3 and older.

Breaking changes and warnings​

New migrate-db container for database migration

In version 23.4, database migration logic has moved to a new container separate from the backend cron container. This generates a better separation of responsibility across various components of the Platform infrastructure. The change is trivial for Kubernetes installations. For Docker Compose, the startup lifecycle of the containers is improved, with better dependency handling among them. See Upgrade steps below for more information to update and migrate your Seqera databases.

Docker Compose V2 supersedes standalone docker-compose for Docker installs

The Docker Compose CLI plugin replaces the standalone docker-compose binary, which was deprecated by DockerHub in July 2023 by Compose V2. The installation documentation now uses the docker compose subcommand for the Docker CLI when using compose files.

Cloud compute environments use cloud cache by default

When a cloud storage location is provided as the pipeline work directory in a cloud compute environment, a scratch folder is created in that location to be used for the Nextflow process cache by default. This can be overridden with an alternate cache entry in your Nextflow configuration.

Login redirection logic update

Login redirection logic has changed in version 23.4. Seqera now prepends the TOWER_SERVER_URL (or tower.serverUrl in tower.yml configuration) to the authentication redirect URL during the login flow. This is useful when your server URL contains a contextual path.

If you specify a DNS name as your TOWER_SERVER_URL, but access your Seqera instance using a different address (such as using an IP address that resolves to the server URL asynchronously), user login will not resolve.

Revert default Tower name changes in documentation

A previous iteration of the rebranded Seqera documentation noted seqera as the default and example value for certain variables (such as default database names). The rebranding from Nextflow Tower to Seqera Platform is an ongoing, incremental process and as such, legacy tower values and naming conventions used by the Seqera backend will remain in place until a future release. Updates to configuration variables and values will be communicated well in advance to prepare users for any breaking changes.

ARM64 CPU architecture support enabled by default

The Use Graviton CPU architecture option is now available by default during AWS Batch compute environment creation. The TOWER_ENABLE_ARM64 configuration environment variable is no longer needed to enable ARM64 CPU architecture support.

Data Explorer default set to false

In previous versions, Data Explorer was enabled by default using TOWER_DATA_EXPLORER_ENABLED=true. From version 2.4.3, the default is TOWER_DATA_EXPLORER_ENABLED=false. If you have upgraded from a previous version and no longer have access to Data Explorer, please check and update your environment variables accordingly.

Upgrade steps​

This version requires a database schema update. Follow these steps to update your DB instance and the Seqera installation.

caution

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.

To upgrade your database schema:

  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 23.4 versions of your deployment templates and update your Seqera container versions:
  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:

  • Apply the database migration:

    • If you use Azure Database for MySQL:

      1. Connect to the database as a role with sufficient privileges to drop a column and run the following query:

        ALTER TABLE tw_label_resource DROP COLUMN IF EXISTS my_row_id;

      2. Run the /migrate-db.sh script provided in the backend container to migrate the database schema.

    • If you use any other database, run the /migrate-db.sh script provided in the backend container to 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>

caution

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.

Seqera Enterprise v23.3

Seqera Enterprise

We're excited to announce that Tower is now Seqera Platform. This name change underscores our vision to evolve Seqera as a single platform for the scientific data analysis lifecycle.

The Seqera platform​

While the underlying platform remains the same, over time you can expect Seqera to become even more scalable, flexible and capable. In the coming weeks and months, references to Tower will be replaced across our product documentation and communications.

We're pleased to announce the availability of Seqera Enterprise 23.3, an important first step in delivering on this revamped product vision and roadmap. Seqera 23.3 includes significant new functionality, including a new Data Explorer, enhanced support for Google Cloud Batch and Google Life Sciences, and much more.

New features​

Data Explorer​

Data Explorer is a powerful new feature of the Seqera platform that lets you easily visualize, search for, and manage data across different cloud providers. This enables you to easily link data to pipelines, troubleshoot runs, and examine outputs - all without switching context. Actions such as file preview, download and upload, as well as custom bucket creation and deletion are logged and details can be accessed in the admin panel.

Data Explorer addresses the scientific community's need to streamline data management for pipelines, from arrival in cloud storage, to diving into the different outputs of a pipeline, and passing data to downstream analysis. We started simplifying this process with datasets, a convenient metadata layer to organize versioned, structured data. Data Explorer is the next big step to enable users to manage their data and analyses in one simple workflow.

Data Explorer simplifies data management across multiple cloud object stores, including Amazon S3, Azure Blob Storage, and Google Cloud Storage. With Data Explorer, organizations can:

  • Browse, search for, preview, or upload data to cloud object stores prior to pipeline submission.
  • Navigate workflow and tasks work directories.
  • Link data to pipelines with a single click.
  • Easily view pipeline outputs or dive into task and working directory data.
  • Pagination of buckets listing and content browsing/listing.
  • Access and view audit logs, and download files.

Data Explorer is accessible via the new Data Explorer tab in Seqera Platform. You can also access the interface to upload files or select datasets and destination storage buckets for pipeline runs.

Other feature improvements​

  • Data Explorer
    • Workspace/global feature toggle.
    • Support uploading files to bucket.
    • Use in launch form path fields.
    • Addition of file select via Data Explorer modal in pipeline launch.
    • Preview text files up to a certain number of lines only.

Enhanced Google Cloud support​

Seqera uses secrets to store the keys and tokens used by workflow tasks to interact with external systems, e.g., a password to connect to an external database or an API token. Seqera relies on third-party secret manager services to maintain security between the workflow execution context and the secret container. This means that no secure data is transmitted from Seqera to the compute environment.

In Seqera 23.3, you can now take advantage of secrets in Google Cloud Batch or Google Life Sciences compute environments by using Google Secrets Manager as the underlying user secrets store.

Pipeline resource optimization​

Pipeline resource optimization allows you to minimize the resources used in your pipeline runs based on the resource use of previous runs.

When a run completes successfully, Seqera automatically creates an optimized profile for it. This profile consists of Nextflow configuration settings for each process and each of the following resource directives (where applicable): cpus, memory, and time. The optimized setting for a given process and resource directive is based on the maximum use of that resource across all tasks in that process.

Other improvements​

  • Implement live events endpoint with WebSockets
  • Permission checker for pipeline launch with simple labels
  • Add support for nf-cloudcache
  • Add Fusion support to Azure Batch
  • Add Fusion support for EKS and GKE platform providers
  • Add support for service account, VPC, and subnet for Google Cloud Batch

Breaking changes and warnings​

Login redirection logic update

Login redirection logic has changed in version 23.3. Seqera now prepends the TOWER_SERVER_URL (or tower.serverUrl in tower.yml configuration) to the authentication redirect URL during the login flow. This is useful when your server URL contains a contextual path.

If you specify a DNS name as your TOWER_SERVER_URL, but access your Seqera instance using a different address (such as using an IP address that resolves to the server URL asynchronously), user login will not resolve.

Revert default Tower name changes in documentation

A previous iteration of the rebranded Seqera documentation noted seqera as the default and example value for certain variables (such as default database names). The rebranding from Nextflow Tower to Seqera Platform is an ongoing, incremental process and as such, legacy tower values and naming conventions used by the Seqera backend will remain in place until a future release. Updates to configuration variables and values will be communicated well in advance to prepare users for any breaking changes.

Upgrade steps​

This version requires a database schema update. Follow these steps to update your DB instance and the Seqera installation.

caution

To ensure no data loss, the database volume must be persistent on the local machine. 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.

  1. Make a backup of the Seqera Platform database.
  2. Download and update your container versions.
  3. Redeploy the application:

Docker Compose:

  • To migrate the database schema, restart the application with docker compose down, then docker compose up.

Kubernetes:

  • Update the cron service with kubectl apply -f tower-cron.yml. This will automatically migrate the database schema.
  • Update the frontend and backend services with kubectl apply -f tower-srv.yml.

Custom deployment:

  • Apply the database migration:

    • If you use Azure Database for MySQL:

      1. Connect to the database as a role with sufficient privileges to drop a column and run the following query:

        ALTER TABLE tw_label_resource DROP COLUMN IF EXISTS my_row_id;

      2. Run the /migrate-db.sh script provided in the backend container to migrate the database schema.

    • If you use any other database, run the /migrate-db.sh script provided in the backend container to 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>

caution

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.

Tower Enterprise v23.2

Seqera Enterprise

New features and improvements​

AWS Fargate support​

Leveraging the Fusion file system, you can now run the Nextflow head job of your pipelines with the AWS Fargate container service. Fargate is a serverless compute engine compatible with Amazon ECS that enables users to run containers without the need to provision servers or clusters in advance. The scalable Fargate container service can help speed up pipeline launch and reduce cloud-related costs by minimizing the time for cloud infrastructure to be deployed.

Other improvements​

  • Add support for Graviton architecture in AWS Batch compute environments.
  • Allow Launcher users to create, edit, and upload datasets.
  • Harmonize list sorting in Compute environments and Credentials list pages.
  • Update Enable GPU label, sublabel and add warning when activated.
  • Set workflow status to unknown when job status is also in an unknown state.
  • Add support for AWS SES (Simple Email Service) as an alternative to SMTP.
  • Add ability to edit the names of Tower entities:
    • Organizations
    • Workspaces
    • Compute environments
    • Pipelines
    • Actions
  • Update runs list page with new status badges and improved layout.
  • Add support for mobile screen layout in runs list page.
  • Allow advanced settings in the AWS ECS config field.
  • Increase the AWS Batch Memory / CPUs ratio to 4GB.

Bug fixes​

  • Disable Resume option for runs that cannot be resumed.
  • Fix task detail modal width.
  • Reserved word checks are now case insensitive.
  • Fix support for AWS SSE encryption for Nextflow head job.
  • Fix race condition causing the "No workflow runs" notice being incorrectly displayed.
  • Fix Pipeline form page breaking during tab reload.
  • Fix an issue resolving Workspace in the Admin panel when several workspaces exist with the same name in different organizations.
  • Fix AWS Batch allocation strategy: BEST_FIT_PROGRESSIVE for on-demand CEs and SPOT_CAPACITY_OPTIMIZED for spot CEs.
  • Fix token creation unique name check is now case-insensitive.
  • Fix issue propagating before: search keywords from Dashboard to runs page.
  • Fix issue with the "copy to clipboard" button using a legacy tooltip implementation.
  • Fix incorrect units displayed for syscr and syscw in task details modal.

Breaking changes and warnings​

Breaking changes and instructions listed here apply when updating from Tower version 23.1. If you are updating from an earlier version, see the release notes of previous versions for a complete picture of changes that may affect you.

Updated AWS permissions policies​

Several new Tower features over the last few releases require updated AWS IAM permissions policies. Retrieve and apply the latest policy files here.

Wave requires container registry credentials​

The Wave containers service uses container registry credentials in Tower to authenticate to your (public or private) container registries. This is separate from your existing cloud provider credentials stored in Tower.

This means that, for example, AWS ECR (Elastic Container Registry) authentication requires an ECR container registry credential if you are running a compute environment with Wave enabled, even if your existing AWS credential in Tower has IAM access to your ECR.

See the relevant container registry credentials page for provider-specific instructions.

Upgrade steps​

This Tower version requires a database schema update. Follow these steps to update your DB instance and the Tower installation.

!!! warning "" To ensure no data loss, the database volume must be persistent on the local machine. 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.

  1. Make a backup of the Tower database.

  2. Download and update your container versions.

  3. Redeploy the Tower application:

    docker compose:

    • To migrate the database schema, restart the application with docker compose down, then docker compose up.

    kubernetes:

    • Update the cron service with kubectl apply -f tower-cron.yml. This will automatically migrate the database schema.
    • Update the frontend and backend services with kubectl apply -f tower-srv.yml.

    custom deployment:

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

Nextflow launcher image​

If you must host your nf-launcher container image on a private image registry:

  1. Copy the nf-launcher image to your private registry.

  2. Update your tower.env with the launch container environment variable:

    TOWER_LAUNCH_CONTAINER=<FULL_PATH_TO_YOUR_PRIVATE_IMAGE>

!!! warning "" 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.

Sharing feedback​

Share your feedback via support.seqera.io.