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Seqera Enterprise v25.3.3

Feature updates and improvements​

Studios​

  • (Public preview) Added SSH connectivity to Studios which enables direct connection to running Studio sessions using standard SSH clients, supporting VS Code Remote SSH and terminal access. See Studios SSH configuration for more information.

Pipelines​

  • Added custom schema support to pipeline versions.
  • Added edit launch pipeline.
  • Enabled custom schema retrieval for pipeline versions.

See Pipeline versioning for more information.

Access Control​

  • Removed participants on workspace deletion.
  • Improved error message when deleting custom roles.
  • Added pagination to roles list page.
  • Added the ability to view an effective permissions summary for any user/workspace combination in the UI or via API.
  • Added the ability to reset a custom role's permissions to match any predefined role (Admin, Maintain, Launch, Connect, View).

Custom roles quota enforcement​

The maxCustomRolesPerOrg quota is now enforced on custom role creation. Organizations at or near their quota limit will be unable to create additional custom roles. Review your organization's custom role usage if you need to create additional roles. Contact support to adjust your quotas if needed.

General​

  • Restored custom navigation menu support in user dropdown.
  • Updated styles for container responsiveness and padding adjustments and footer.
  • Added only current page in task pagination.
  • Added storage for SSH public keys for use in Studios.

Bug fixes​

  • Cleared parameters when changing between pipeline with and without parameters.
  • Fixed correctly updated versions list when version is published.
  • Prevented re-assignations of pipeline.launch when working with versions.
  • Updated schema when schemaName field value changes.
  • Prevented adding empty parameters when reseting parameters form with defaults after config profile change.

Upgrade steps​

This release maintains backward compatibility with version 25.2.x.

note
  • Make a backup of your Platform database prior to upgrade.
  • If you are upgrading from a version prior to 25.1, complete all intermediate major version upgrades before upgrading to 25.3.
  • Ensure that no pipelines or Studio sessions are in a running state during this upgrade as active run data and analysis may be lost.

See Upgrade deployment for installation guidance.

Fusion v2.4.20

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.4.20-amd64.json'
}
info

For ARM64 CPU architecture, use containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.4.20-arm64.json'.

Feature updates and improvements​

Fusion Snapshots​

  • Added support for Fusion Snapshots in Google Batch. See Fusion Snapshots for more information.
  • Added cleanup for dump folder following Spot termination to prevent unwanted storage costs.

Logging​

  • Better log readability: Added [seqera-fusion] prefix to console logs for easier identification in mixed output environments.
  • Improved error messages: Added more context and clearer wording to cloud provider errors, including better messages for archived/cold storage objects.

Troubleshooting​

Bug fixes​

AWS​

  • Fixed misleading "file not found" errors: Changed permission errors (403 Forbidden) from cloud providers to display as "Permission denied" instead of incorrectly showing "No such file or directory" (#1068).

General​

  • Cloud errors now log properly: Fixed an issue where cloud service errors were silently treated as simple "file not found" cases instead of logging and reporting properly (#1077).

Upgrade notes​

  • Drop-in replacement for v2.4.x. No configuration changes required.

Fusion v2.5.9

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.9-amd64.json'
}
info

For ARM64 CPU architecture, use containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.9-arm64.json'.

Feature updates and improvements​

Fusion Snapshots​

  • Added support for Fusion Snapshots in Google Batch. See Fusion Snapshots for more information.
  • Added cleanup for dump folder following Spot termination to prevent unwanted storage costs.

Logging​

  • Branded console logs: Added [seqera-fusion] prefix to all console logs for better identification in mixed output environments.
  • Real-time terminal output: Changed command output to display immediately in the terminal instead of buffering, improving visibility during execution.
  • Clearer error messages: Improved error messaging for non-recoverable I/O errors and archived objects.

Troubleshooting​

Bug fixes​

AWS​

  • Fixed AWS S3 Forbidden errors not mapping properly to permission denied.

General​

  • Fixed cloud storage errors not logging properly in certain scenarios.

Upgrade notes​

  • Drop-in replacement for v2.5.x. No configuration changes required.

Nextflow 25.10.3

Feature updates and improvements​

  • Added Channel::mix(Value...) by @bentsherman in a2bb57158
  • Added spot interruption tracking to trace records by @munishchouhan in #6606

Bug fixes​

  • Fixed nextflow inspect not applying container settings from config by @ewels in #6736
  • Fixed false error with task ext blocks in strict syntax by @bentsherman in #6569
  • Fixed issue with topic file emissions in typed processes by @stekaz in #6688
  • Fixed optional param in params block by @bentsherman in #6657
  • Fixed validation of numeric types in params block by @bentsherman in #6656
  • Fixed ignore multi-revision folder in list command by @jorgee in #6678

Dependencies​

  • Bumped nf-amazon@3.4.3
  • Bumped nf-google@1.23.4
  • Bumped nf-tower@1.17.4

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.3

Seqera Cloud v26.1.0_cycle38

Feature updates and improvements​

Studios​

  • Added feature detection for one-time token support in Studios to determine whether to send deprecated long-lived tokens to the client.

Compute environments​

  • Fixed compute environment listing failures for legacy Seqera Compute Batch configurations that don't implement IAwsCloudConfig.
  • Fixed compute environment listing when requesting attributes for deprecated platforms.
  • Fixed validation to enforce the default m5d.large instance type for Seqera Compute environments.

Pipelines​

  • Implemented transparent hash version upgrade mechanism that automatically detects and upgrades outdated pipeline version hashes during comparison operations without persisting changes.
  • Implemented VersionedHash class to provide structured, type-safe access to version hash strings throughout the platform, improving code maintainability and enabling future hash algorithm upgrades.
  • Removed the pipeline_version_created audit event in favor of the existing pipeline_updated event, which already tracks pipeline version creation.

Permissions and roles​

  • Added tristate checkboxes to category rows in the custom roles permissions table, allowing users to quickly select or deselect all permissions within a category.
  • Consolidated Members, Teams, and Collaborators pages into the Access Control page as tabs with pagination support for Teams list and empty-state components.
  • Added admin endpoint GET /api/admin/orgs/{orgId}/roles to list organization roles.
  • Added endpoint GET /orgs/{orgId}/users/{userId}/roles to list user roles in organization.
  • Added maxCustomRolesPerOrg quota definition and enforcement, limiting the number of custom roles per organization.

Data Explorer​

  • Fixed file preview functionality for files containing special characters (brackets) in filenames by properly encoding and decoding file paths.

Bug fixes​

  • Fixed Open in new tab functionality for workflow reports by implementing a separate route with report path passed as query parameter.
  • Fixed step status indication mechanism in launch forms to properly track all controls registered to a section, including those registered after initial creation.
  • Fixed Data Explorer path decoding to be null-safe, preventing test failures.
  • Fixed an issue causing custom pipeline info fetch error messages to be incorrectly removed when selecting the same value again in pipeline, revision, or main script fields.
  • Fixed an issue causing the Launchpad to display empty optimization buttons when optimization status is not set.
  • Prevent conda Studios from auto-starting when the organization exceeds Studio session limits.

Seqera Cloud v26.1.0_cycle37

General updates and improvements​

Studios​

  • Added validation to ensure the workspace container repository setting is configured before allowing creation of custom-built Studios.
  • Added Studios to the onboarding resources shown to new users during account setup, helping users discover Studio functionality early in their journey.
  • Removed the ability to start and stop Studios from the Launch role to better align permissions with user responsibilities.

Compute​

  • Added Amazon EC2 p6-b300 instance family to the NVMe storage list, enabling support for this new GPU-optimized instance type.
  • Added the ability to disable and enable compute environments through the UI. This allows administrators or workspace owners to temporarily or permanently prevent new workflow executions or new Studio sessions on disabled compute environments.
  • Introduced error messaging when attempting to launch workflows on disabled compute environments. The error message now explicitly states Specified compute environment disabled instead of the generic Not available message.
  • Added Amazon EC2 X8aedz memory-optimized instance family (powered by AMD EPYC processors) to the NVMe storage list, supporting up to 8 TB of local NVMe SSD storage.
  • Updated the default Azure Batch image and improved error propagation for image-related failures.

Workflows​

  • Added tracking for Spot instance interruptions (numSpotInterruptions) at the task level, aggregated to the workflow level. This metric tracks how many times Spot instance preemption interrupted and restarted tasks.

Launchpad​

  • Renamed Config view to Params file view in launch form parameters, to align terminology with Nextflow.

Bug fixes​

Studios​

  • Fixed an issue that allowed basic organizations to run more than one Studio simultaneously. Basic organizations now default to a maximum of 1 running Studio when not setting an explicit quota, while other organization types use the global limit (default: 100).

Compute​

  • Fixed intermittent workflow launch failures caused by cache returning expired AWS STS credentials. Added expiration checking, configurable refresh margin, and cache invalidation for expired entries.
  • Reverted Azure Batch to use Ubuntu 22.04 (from 24.04).
  • Fixed errors when listing compute environments with the resources attribute for legacy Seqera Compute Batch configurations that don't implement IAwsCloudConfig. Added proper handling and fallback logic.

Pipeline versioning​

  • Fixed an issue with pipeline version lists not updating correctly when publishing a draft version.

Launchpad​

  • Fixed an issue with parameters not clearing correctly when switching between pipelines with and without parameters in the launch form.
  • Fixed date formatting to use calendar year (yyyy) instead of ISO week-based year (YYYY), which caused dates at year boundaries to display the wrong year.
  • Fixed the merging of entity and compute environment labels for single VM compute environments to ensure labels are properly combined and applied.

Fusion v2.4.19

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.4.19-amd64.json'
}
info

For ARM64 CPU architecture, use containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.4.19-arm64.json'.

Feature updates and improvements​

Snapshots​

  • Platform-specific snapshot detection: Added instance type detection for granular snapshot support; updated Fusion Snapshots to v1.8.0.
  • Incremental dumps enabled by default: Snapshots incremental dumps now run automatically.

GPU​

  • GPU tracer backport: Backported GPU tracer feature from master.

Bug fixes​

General​

  • Idempotent Remove operations: Fixed race conditions in concurrent rename operations by making Remove() idempotent across all cloud providers (GCS, S3, Azure)

Upgrade notes​

Drop-in replacement for v2.4.x. No configuration changes required.