74 posts tagged with "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.

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.

Seqera Cloud authentication updates​

Seqera Platform Cloud has migrated to a new authentication provider, which includes two major changes to the login flow.

Passwords for email login​

• Users signing in via email: The next time you sign in to Seqera Cloud, select the option to create a new account — "Create one" — and add a password for your existing account. The system will preserve all your existing account information and you can complete all future sign-ins with your new password.

• Users using Github/Google sign-in: You are not required to define a password for your account and shouldn’t see any changes on your next sign-in.

Account linking​

Users that sign in with multiple accounts associated with the same email address: You will be prompted to optionally merge your accounts into a single account. This will merge all your work across the two different accounts into the same account and give you the option to sign in via either method of authentication.

If you choose not to merge accounts, you will not be prompted again. If you wish to merge accounts later, or would like to merge accounts with different email addresses, contact Seqera Support.

Feature updates and improvements​

Studios​

• Data Studios now support GPUs.
• Augment Data Studios images with custom Conda environment.
• Data studio creation now includes YAML validation.
• Data Studios build stats now appear in the Dashboard.
• New data studios now include "Add only" and "Add and start" actions.

Pipelines​

• The pipeline parameters input form now supports JSON schema draft 2020-12.

Bug fixes​

Studios​

• Data Studios UI fixes.
• Improved Data Studios error messaging.
• Deleted Data Studio checkpoint on build failure.
• Updated default Data Studios tool versions.
• Failed Data Studios can now be deleted.
• Return an empty list of data studios when receiving an invalid status.

General​

• Added back to login button in authentication error screen.
• Added custom token cookie login handler for Nextflow requests to receive authentication cookies.
• Jedis connection pool config which caused potential instabilities.
• Fixed a problem with Azure Entra credential creation.

Launchpad​

• Set launch form to parameters step view by default when a pipeline schema is present, regardless of specification.
• Fallback to primary compute environment when launching a shared pipeline without an associated compute environment from a private workspace.

UI/UX​

• Dashboard persisted filters exclude workspace IDs the user no longer has access to.

Pipelines​

• Do not fetch info for INVALID status pipelines, fetch for all other statuses including DISABLED.

Feature updates and improvements​

Studios​

• Data Studio sessions can now share mounted data across the same workspace.
• New dashboard for Data Studios.

Launchpad​

• Quick Launch now accepts pipelines that do not have a branch named master.
• The new Launch Form now appears in Quick Launch and personal workspaces.

Compute environments​

• Improved fetching of the cloud cost estimation for Google Cloud Platform's (GCP) spot instances.
• ECS container timeout configuration is now set to 10 minutes by default (ECS_CONTAINER_CREATE_TIMEOUT=10m,ECS_CONTAINER_STOP_TIMEOUT=10m,ECS_MANIFEST_PULL_TIMEOUT=10m).

General​

• Improved query times on some clean up job queries.
• NF Launcher image is now pulled by default from cr.seqera.io public registry instead of quay.

Bug fixes​

Pipelines​

• If the revision was not specified in Quick Launch, schemas did not fetch correctly.

Compute environments​

• Retrieving managed identity IDs on updates resulted in the system displaying the incorrect managed identity.

Studios​

• Start in new tab from the Data Studio form didn't navigate back the main tab to Data Studios page.

Feature updates and improvements​

Studios​

• Added direct Data Explorer browse link to mounted data items.
• Made Studio details page tabs routable.

Data Explorer​

• Highlight invalid custom datalinks.
• Removed folder validation.

Compute environments​

• Updated Azure service principal credentials.
• Disabled AWS and Google Batch spot instance auto retry.

Workflows​

• Patch workflow revision.

Launchpad​

• Render Parameters UI correctly with new schemas based on 2020-12 draft.
• Pipeline launch form: Delegate form creation to a form builder service.

API​

• Updated 204 pipeline schema response description.

General​

• Defined cache configuration once, only override changes.
• Upgraded to Angular 16.

Bug fixes​

General​

• Connection to Redis SSL server.
• Terminated by Tower error.

API​

• pairingId declaration in API schema.

Data Explorer​

• Copying empty list for cloud data links.
• Datalink status always null.

Launchpad​

• Visual glitches in launch form.

Studios​

• Updated last used field in compute environment when creating a data studio job.