47 posts tagged with "seqera cloud"

Bug fixes​

General​

• Fixed an issue in Firefox where login resulted in an infinite loop in the browser.

Version bump​

• Bumped Nextflow launcher to 25.04.x.

Seqera Compute​

Seqera Compute is now in public preview. Seqera Compute is a fully managed, optimized compute environment which eliminates infrastructure complexity by automating environment setup, resource provisioning, scaling, and optimization.

Platform interface updates​

Pipeline run details​

Refreshed the pipeline run details page with improvements such as:

• Clear, dynamic view of pipeline execution in real time via a progress bar.
• A dedicated Run info tab with a centralized view of run metadata and status details.
• Improved navigation tabs for Tasks, Logs, Metrics, and Containers.

New Seqera Platform sidebar​

Replaced the Platform top navigation with a sidebar for improved navigation.

AWS Cloud compute environment​

The new AWS Cloud compute environment supports faster startup time, simplified configuration, and fewer AWS dependencies. Using this compute environment, Studios can now be launched on Spot instances. The AWS Cloud compute environment is best suited to run Studios and small to medium-sized pipelines. It offers more predictable compute pricing, given the fixed instance type. It spins up a standalone EC2 instance and executes a Nextflow pipeline or Studio session with a local executor on the EC2 machine. At the end of the execution, the instance is terminated.

API documentation improvements​

Updated the Seqera Platform API documentation. Featuring overview pages with parameter and request body tables, categorized by Platform entity (compute environments, pipelines, etc.), the documentation now provides easier reference and detailed request examples.

Other new features and improvements​

Compute environments​

• Added Fusion snapshots to AWS Batch.
• Enabled DRAINING status for Spot instance reclamation. When an instance is in DRAINING status, no new task can be scheduled on it. See Configuring Amazon ECS Linux container instances to receive Spot Instance notices for more information.
• AWS Cloud compute environment defaults to the public Seqera AMI when not specifying an AMI ID during compute environment creation.

Studios​

• Added Spot option for AWS Cloud compute environment.

Pipelines​

• Supported markdown rendering for Nextflow object field help_text and description properties.

Feature updates and improvements​

• Fusion
  • Added 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​

Workflows​

• Fixed container table pagination.
• Made task-level containers tab visible only when containers are available.

Launch form​

• Fixed a launch form issue with eager parameter keyword interpolation.

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.

Compute environments​

• Changed the default for the single VM compute environment to the Seqera-optimized AMI. When not specifying an AMI during compute environment creation, the system defaults to the Seqera-optimized AMI.

Workflows​

• Added a more detailed warning for workflow cleanup issues that are related to access restrictions to the AWS Batch compute environment.
• Added task status badges with icons to the workflow run tasks table.

Launchpad​

• Added support for array type parameters in the Launch form.
• Implemented support for multiple extension dataset parameters in the input form.
• Show Nextflow config parameters that are binary expressions in the Launch form.

API​

• Added azure_entra to the provider list of credentials in the OpenAPI spec.

General​

• Delete pipeline secrets in the user context from the provider.
• Switch logs, secrets-manager, marketplace-meter, and simple-email dependencies to AWS SDK v2.
• Switched AWS S3 to SDK v2.

Bug fixes​

General​

• Modify cache expiration policy to resolve "Connection pool shut down" error with new AWS SDK v2 clients.

Workflows​

• Fixed an issue where the workflow details page displayed the Edit Labels button even when there were no labels, but the workflow had attached resource labels.

Launchpad​

• Fixed an issue where the Quick Launch form did not select the primary compute environment by default.

Feature updates and improvements​

Compute environments​

• Updated the default Azure Batch Ubuntu image to SKU 22.04 to avoid issues with the existing image (SKU 20.04), which will be deprecated after April 23, 2025. For more information about the deprecation, see https://github.com/Azure/Batch/issues/174.

Feature updates and improvements​

Studios​

• Private sessions: When adding a new session, the number of concurrent connections can now be defined in General Config > Collaboration.
• Dynamic Studio templates: Added labels to indicate the status of support (e.g., Recommended, Deprecated) for a Studio template version. Users can now also switch the Studio's base template image when starting a session as new.

Pipelines​

• Updated WfManifest class to include the new icon property introduced in Nextflow.
• Added a new migration file to add the new icon column into all the tables of entities that use the WfManifest class as @Embedded property.
• Supported image upload in the pipeline import and pipeline update forms for use as pipeline logos.

Audit logs​

• Audit log update: The system now logs pipeline edit events.

Workflows​

• Added totalProcesses count to workflow progress responses.
• New workflow job monitoring collects and publishes Platform metrics.

Compute environments​

• Switched AWS Batch compute environment dependencies to AWS SDK v2.

Bug fixes​

Studios​

• Fixed a bug where resource labels erroneously allowed users with the maintain role to edit them when starting an existing Studio.

Compute environments​

• Fixed a potential NullPointerException on code related to Google Batch, where the method is expected to return null.

UI/UX​

• Fixed an issue where users could not remove the organization logo.

Feature updates and improvements​

Studios​

• Added Studio session lifespan setting. This feature allows you to set a lifespan for a session, after which the system automatically stops the session.
• Added Studios resource labels support. Workspace admins and owners can edit resource labels inherited from the compute environment and apply them to a Studio session. The edited resource labels associated with each session don't affect the default resource labels associated with the compute environment.

Permissions and roles​

• Reduce the maximum number of organization members to 3.
• Resource tracking in the Platform UI for improved management of free tier limits.
• Added user disable/re-enable support.

Compute environments​

• AWS Batch compute environments default to Amazon Linux 2023 AMI when enabling Fusion v2
• Set ECS_CONTAINER_START_TIMEOUT to 10 minutes in the ECS settings used by AWS Batch CEs in order to prevent the error Task failed to start - DockerTimeoutError: Could not transition to started; timed out after waiting 3m0s.

Workflows​

• Implemented collapsible view for JSON workflow parameters tab and add View as YAML option.
• Mark long-running jobs with a warning: This warning displays when a workflow has been in the RUNNING state for more than 3 hours and no single task has moved from one state to the next.

Pipelines​

• Updated the pipeline name regular expression to allow pipeline names containing dots ('.').

General​

• Notified the user when secrets cleanup fails.
• Upgraded to Angular 18

Bug fixes​

Studios​

• Fixed an issue with searches for names containing special SQL wildcard characters (_, %).
• Fixed an issue to ensure that the Maintain role is not able to change resource labels inherited from the selected compute environment when adding/starting a Studio.

Feature updates and improvements​

Studios​

• Display the applied date filter on the Dashboard page.
• Added support for custom templates for input control options such as workspace visibility and session lifespan.

Compute environments​

• Default to Amazon Linux 2023 AMI when enabling Fusion v2.
• Added support for Fusion licensing.

Workflows​

• Extend zombie jobs detection on all workflows reaching one of the terminal states (SUCCEEDED, FAILED, CANCELLED).

Launchpad​

• Allow Nextflow configuration parameters with embedded references to other parameters to be shown verbatim.

UI/UX​

• Implemented FaviconService that changes the favicon based on pipeline run or Studio status.

General​

• (Enterprise only) Added a job to save usage metrics to files so users can access and share usage data even when they're not connected to License Manager.
• Increase accessTokenExpirationTime by 10% to always trigger a token refresh when Platform is open in a browser tab that isn't hibernated.

Bug fixes​

API​

• Fixed an additional reference to the mainScript parameter in the pipeline-info API response.

General​

• Improved security of passthrough redirection on Platform authentication.

Breaking changes​

• Restore errorStrategy and maxRetries default Nextflow config for AWS and GCP launches. Platform will not overwrite existing error strategy coded in the pipeline repository.
• If you want to automatically retry on task failures (e.g., from spot reclamations), you will now need to explicitly set errorStrategy and maxRetries.
• Automatic spot retries in AWS and GCP now require active enablement. Alternatively Nextflow handles the generic failure at the Nextflow level.

You can revert to the default setting used in Nextflow prior to 24.10 with the following configuration options:

aws.batch.maxSpotAttempts = 5
google.batch.maxSpotAttempts = 5

Set task.maxRetries to a non-zero value to restore Platform to prior behaviour.

How do I retry Spot failures while making them visible?

There is no mechanism in Nextflow to specifically report Spot retries. However you can set process.maxRetries = 5 to retry all failures (including Spot reclamations) a specified number of times before failure.

Feature updates and improvements​

Studios​

• Added data studio API endpoints to the OpenAPI spec.

Permissions and roles​

• New organization types added to allow free tier users to monitor their usage and limits.

Workflows​

• Restore errorStrategy default Nextflow config for AWS and GCP launches. The Nextflow job now correctly terminates after pipeline completion.
• The system now automatically terminates Azure jobs after all tasks complete.

Compute environments​

• Updated list of EC2 families with NVMe disks available.

Launchpad​

• Send only added/updated run parameters when launching a pipeline. This includes all defaults and parameters passed during the launch.

Pipelines​

• Improved error messaging when pipeline info can't be fetched indicates whether the issue is due to a missing resource, or failed authentication due to expired credentials.

UI/UX​

• New dynamic page title for easy bookmarking.

General​

• Upgraded to Angular 17
• Bumped Nextflow launcher to 24.10.3

Bug fixes​

Pipelines​

• Allow unsetting schemaName when editing a pipeline.
• Take into account the alternative mainScript path.

General​

• Use preferred_username as fallback email field for OIDC login.
• Drop the last characters in job definition name, if longer than the prescribed limit.
• Prohibited duplicate Git credentials and added tie-break on lastUpdated for existing duplicates. Going forward, the system gives preference to the credentials updated last when multiple candidates exist. Additionally added a duplicate check when creating new credentials, to avoid new duplicate cases.

Compute environments​

• Compute environment creation form allows pre- and post-run scripts to be longer than the accepted value of 1024 characters.

Workflows​

• Disabled reset selection on data change in workflow list component.

Feature updates and improvements​

Compute environments​

• Added AWS Forge support for Amazon Linux 2023.
• Deprecated Google Life Sciences API.

Studios​

• Added name validation to custom containers during Data Studio session creation.

Workflows​

• Refactored reports file streaming over Agent connections.

General​

• Bumped Nextflow launcher to 24.10.0.

Bug fixes​

Compute environments​

• Propagate EFS mount path to container volume.

Launchpad​

• Include optimization data to launch request, if present.
• Input form view not working for private GitHub repos during pipeline quicklaunch.
• Workspace secrets not selected by default during pipeline quicklaunch with new launch form.
• Apply the old launch form behavior to the new launch form when launching a shared pipeline from a private workspace.

Studios​

• Added missing permissions check to data studio checkpoint "Start as new" option.
• Added volumes to data studio job definition.

Resource labels​

• Users with "Maintain" role and lower can edit resource labels when launching with the new pipeline launch form.

UI/UX​

• Correctly update user through profile page.
• Improved layout on large displays.
• Do not register the "User" route when disabling the user personal workspace.

General​

• Improved error messaging for expired Git credentials.