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Seqera Cloud v26.1.0_cycle41

Feature updates and improvements​

Access control​

  • Added Duplicate button to Roles page, allowing users to create new roles based on existing role permissions.

Pipelines​

  • Refactored default pipeline version handling by removing ensureDefaultVersion support and improving version management logic.
  • Added new pipeline version update endpoint (POST /pipeline-versions/{versionId}) for updating specific pipeline versions independently from the default version.
  • Fixed PipelineVersionLaunchComposite query logic to properly return null for non-existent pipeline versions instead of creating invalid composite objects.

Compute environments​

  • Updated default Azure Batch VM image to Ubuntu 24.04 (SKU 2404).

General​

  • Added custom schema support to pipeline forms, allowing users to specify custom schema names or URLs for pipeline configuration.
  • Added centralized design system tokens (tokens.ts) with functional colors, semantic colors, and component sizes for consistent UI styling.
  • Added auto-detection of form controls in ExpansionPanelComponent via the new wtExpansionPanelDetail directive, reducing boilerplate code and enabling reactive updates to collapsed panel summaries.
  • Enabled custom pipeline schema retrieval via the /pipelines/{pipelineId}/schema endpoint, with improved error handling and refactored transaction management.

Nextflow 26.01.0-edge

Feature updates and improvements​

Language features​

  • Allowed collection-type params to be loaded from files by @bentsherman in #6675
  • Enabled v2 syntax parser by default by @bentsherman in #6643
  • Improved config syntax errors by @bentsherman in #6721
  • Improved error message for invalid config statements by @bentsherman in #6804
  • Improved error messages for workflow outputs by @bentsherman in #6785
  • Moved task hashing logic to TaskHasher class by @bentsherman in #6572

AWS Batch​

  • Added aws.batch.forceGlacierTransfer config option by @munishchouhan in #6700

Google Batch​

  • Refactored GoogleBatchTaskHandler.newSubmitRequest for reduced complexity by @pditommaso in #6687

Kubernetes​

  • Added time-based caching for K8sConfig.getClient() by @munishchouhan in #6742

Configuration​

  • Supported multiple config option types in config spec by @bentsherman in #6720

General​

  • Added accelerator request to trace record by @munishchouhan in #6703
  • Added CloudCacheConfig to register cloudcache config options by @pditommaso in #6774
  • Added markdown output mode to lint command by @ewels in #6715
  • Added missing provider credentials when updating the bare repo in multi-revision assets by @jorgee in #6698
  • Added warning stats to lint summary output by @ewels in #6714
  • Added workflow manifest metadata to execution report by @bentsherman in #6689
  • Detected conda explicit files by content instead of extension by @bentsherman in #6713
  • Excluded nf-test.config from lint by default by @ewels in #6716
  • Used conda-forge and bioconda channels by default by @Midnighter in #5423

Dependencies​

  • Bumped Groovy to 4.0.30 by @pditommaso in #6747
  • Bumped Spock 2.4 by @pditommaso in #6681

Bug fixes​

Language features​

  • Fixed caching of task ext properties with the strict parser by @bentsherman in #6696
  • Fixed compiler error in v2 parser with enums by @bentsherman in #6781
  • Fixed different task hash with v2 parser by @bentsherman in #6789
  • Fixed false error in v2 parser when including config file from http url by @bentsherman in #6753
  • Fixed false error with multi-line tuple assignment in v2 parser by @bentsherman in #6786
  • Fixed false error with optional param by @bentsherman in #6811
  • Fixed issue with topic file emissions in typed processes by @bentsherman in #6688
  • Fixed params inclusion across modules in v2 parser by @bentsherman in #6766
  • Fixed resolution of nested Groovy class in v2 parser by @bentsherman in #6744
  • Fixed type inference in v2 ConfigDsl by @bentsherman in #6800

AWS Batch​

  • Fixed AWS Batch spot instance detection by @munishchouhan in #6722
  • Fixed isCompleted check in getNumSpotInterruptions by @munishchouhan in #6805

S3​

  • Fixed error when checking whether an S3 bucket exists by @jorgee in #6706

Kubernetes​

  • Fixed K8s job fallback to not return incorrect zero exit code by @munishchouhan in #6746

General​

  • Fixed fetching new remote branch in multi-revision mode by @jorgee in #6733
  • Fixed lint error formatting for errors at end of line by @ewels in #6717
  • Fixed LogsCheckpoint thread blocking shutdown for up to 90 seconds by @pditommaso in #6787
  • Fixed nextflow inspect not applying container settings from config by @adam-novak in #6736
  • Fixed spurious WARN when workflow fails before onFlowBegin by @pditommaso in #6816

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.01.0-edge

Seqera Cloud v26.1.0_cycle40

Feature updates and improvements​

Compute environments​

  • Allowed arbitrary Security Group/subnet values and improved error feedback.

Pipelines​

  • Changed to only show current page number of workflows pagination.
  • Added template role selector to custom role form.
  • Added custom schema add edit launch pipeline.

Data Explorer​

  • Implemented member details screen.
  • Removed participants on workspace deletion.
  • Improved error message when deleting custom roles.

General​

  • Assigned pipeline.launch to the default version.

Bug fixes​

User interface​

  • Fixed incorrect icons displayed throughout the application.
  • Fixed Role View page paddings.
  • Fixed cost estimates to display with 2 decimal places for consistency.
  • Improved tasks table default pagination from 10 to 25 items.

Workflows and pipelines​

  • Fixed pagination state loss when navigating back to workflow and task lists.
  • Fixed pipeline launch configuration being incorrectly reassigned when working with pipeline versions.
  • Fixed empty parameters being added after changing configuration profiles.

Studios​

  • Fixed error handling when Studio version information is unavailable.

Access control​

  • Fixed SSH key creation failing due to missing ID generator.

Seqera Cloud v26.1.0_cycle39

Feature updates and improvements​

Access control and roles​

  • Consolidated user and team management into an Access Control menu.

Pipeline and workflow management​

  • Added operation to delete from workspace by userId.
  • Support keywords to search pipeline versions by name and hash.
  • Added username dynamic resource label placeholder for workflow labeling.

User interface​

  • Added CE_FORMS_V2 compute environment form page.
  • Show only current page in task pagination.
  • Implement advanced search help popover in version list.

Bug fixes​

Data Explorer​

  • Fixed data links not displaying until all are fetched - now shows incremental loading.

Studios​

  • Enable Fusion in Azure Batch with Ubuntu 24.04 by installing custom AppArmor profile.
  • Studio no longer throws error when failing to fetch Studio connect-client version label.

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.