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Changelog

Seqera Enterprise v25.3

Seqera Enterprise

Seqera Platform Enterprise version 25.3 introduces a series of new features and enhancements, including custom user roles, Studios integration with Git providers, and pipeline versioning.

New features and improvements​

Custom roles and fine-grained authorization (RBAC)​

  • Added support for custom roles with fine-grained permissions, to define specific access controls beyond the predefined Owner, Admin, Maintain, Launch, View, and Connect roles.

Studios​

  • Updated the Add Studio page to a single-step form.
  • Added support for Azure single VM compute environments.
  • Added support for loading Studio configuration from private and public Git repositories.
  • Added ability to clone content from a Git repository to a Studio at startup time.
  • Added ability to create Studios from Docker images, built from a repository Dockerfile using Wave.
  • Added ability to stop a Studio session that is stuck starting without needing AWS console access.
  • Added Save as data link action when mounting data to a Studio.
  • Added support for custom environment variables to Studio configuration.

Pipelines​

Datasets​

  • Refactored datasets list and detail views with additional metadata and improved version control.
    • Added ability to dynamically show/hide datasets for all users in the workspace. Hidden datasets do not consume workspace quota.
    • Removed dataset quota limits.
    • Added ability to sort dataset list by name, recently updated, and recently used.
    • Added support for labels.
    • Enhanced filtering of all dataset attributes (visibility, label, username, createdAfter, createdBefore, updatedAfter, updatedBefore, usedAfter, usedBefore).
    • Added one-click view of all pipeline runs using a specific dataset, adding direct traceability between datasets and workflow runs.

Data Explorer​

  • Added support for S3-compatible object storage providers. To use additional object storage providers, update the unprivileged CSP policy.
  • Added support for LakeFS Cloud in Data Explorer by enabling image preview and file upload functionality when using LakeFS Cloud as an S3-compatible storage provider.
  • Added CSP config for OCI Object Storage, Cloudflare R2, and LakeFS Cloud.

Compute​

  • Configured Nextflow to automatically terminate unschedulable jobs on AWS Batch compute environments by setting aws.batch.terminateUnschedulableJobs to true by default. This prevents jobs that cannot be scheduled (due to invalid resource requests or configuration errors) from indefinitely blocking the job queue.
  • Implemented safeguards to prevent unschedulable jobs from blocking other jobs in the queue. When jobs cannot be scheduled due to resource constraints or configuration errors, they are handled separately to ensure other valid jobs can proceed.
  • Added the AWS g6e instance family (NVIDIA L40S GPUs) to the NVMe disk support list, enabling high-performance instance storage for GPU-accelerated workloads.
  • Added f2.6xlarge, f2.12xlarge, f2.48xlarge instance types.
  • Extended Google Cloud config with selectable Advanced options - machineType, image, armEnabled.

Nextflow launcher image​

If you 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 following environment variable:

TOWER_LAUNCH_CONTAINER=<FULL_PATH_TO_YOUR_PRIVATE_IMAGE>

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.

General​

  • Bumped Nextflow launcher to nf-launcher:j21-25.04.8.
  • Replaced the top navigation with a sidebar in Platform.
  • Updated Platform behavior to redirect to first available sidenav item instead of hardcoded launchpad.
  • Added usage statistics to the Datasets API, allowing you to view the number of pipeline runs using each dataset and when it was last used.
  • Added metrics to confirm whether a pipeline is running GPU resources.
  • Added better support for treating Nextflow config preferentially, as mono-repo configurations are now read from the same directory as the configured main script.
  • Added support for BitBucket API tokens to ensure that Bitbucket can still be used as an API provider. See the announcement for more information: https://bitbucket.org/account/settings/app-passwords/.

Bug fixes​

  • Fixed Studios AWS cloud private ECR pull issues.
  • Fixed handling of Studios tokens without user ID claim.
  • Fixed MultiQC plots displaying as grey boxes.
  • Fixed badge cropping issues in Platform UI.
  • Fixed infinite scroll in optimization profile modal.
  • Removed blanket ListOrganizationSettings check, use individual permissions instead.
  • Added proper permission checks for workflow star functionality.
  • Forced perfect circle avatar shape for consistent rendering.
  • Fixed pipeline list not updating when changing workspace.
  • Prevented incorrect workdir patching when resuming workflow with compute environment changes.
  • Fixed pipeline config reading from same directory as main script.
  • Fixed error when saving long container names.
  • Fixed trigger YAML validation on Studios config patch.
  • Fixed describePipeline to properly handle avatar files.
  • Fixed transactional event listener annotation for compute operations.
  • Improved Connect parameter handling for compute environments.
  • Fixed OIDC API handling in authentication flows.

Fusion​

See the Fusion changelog for more details.

Wave​

See the Wave changelog for more details.

Nextflow​

See the Nextflow migration notes page for changelog details.

MultiQC​

See the MultiQC changelog for details.

General warnings​

Starting from version 26.1, the front end image running as root user will be deprecated. We recommend starting to switch to the root-less image (also known as "unprivileged" image) during this upgrade. See Kubernetes and docker-compose deployment documentation for instructions.

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 are in a running state during this upgrade as active run data may be lost.

See Upgrade deployment for installation guidance.

Wave v1.30.0

Wave

Feature updates and improvements​

  • Add configurable Singularity init container image by @pditommaso in #937
  • Use Seqera-hosted buildkit image by @pditommaso in #938
  • Add labels in ConfigSpec by @munishchouhan in #934

Bug fixes​

  • Fix typos in Wave Kubernetes install by @christopher-hakkaart in #930
  • Fix scan and mirror enabled flag bug by @munishchouhan in #935
  • Fix wave.scan.enabled feature flag and YAML indentation by @pditommaso in #936

Full changelog: https://github.com/seqeralabs/wave/compare/v1.29.1...v1.30.0

Seqera Cloud v25.3.0_cycle31

Seqera Cloud

General updates and improvements​

  • Data Explorer
    • Added support for LakeFS Cloud in Data Explorer by enabling image preview and file upload functionality when using LakeFS Cloud as an S3-compatible storage provider.
  • Improved job failure handling in AWS Batch compute environments. Improved AWS Batch workflow behavior to automatically terminate unschedulable jobs instead of leaving them pending indefinitely, providing faster feedback when compute resources are insufficient for workflow requirements.
  • Added the g6e instance family to the list of AWS instances with NVMe storage.

Bug fixes​

  • Fixed an issue where plots and charts in MultiQC reports appeared as grey boxes instead of displaying correctly, ensuring all visualizations now render properly. MultiQC reports generated by pipeline runs now display complete quality control metrics and interactive charts without missing content.
  • Fixed an issue where YAML validation errors were not displayed immediately when importing Studio configurations from Git repositories, ensuring configuration issues are now visible as soon as the import completes.
  • Fixed an issue where AWS single VM compute environments could not pull container images from private Amazon ECR repositories, bringing them to feature parity with AWS Batch compute environments.
  • Fixed an issue with older pipeline launch records, where the source type had not been set properly, resulting in failure to access the pipeline entity on launch.

Seqera Cloud v25.3.0_cycle30

Seqera Cloud

General updates and improvements​

  • Improved label inheritance when launching workflows via API to automatically apply predefined labels when the labelIds field is omitted, aligning API functionality with the GUI and simplifying workflow relaunches.

Bug fixes​

  • Fixed an issue where changing the compute environment during workflow resume incorrectly updated the work directory path, causing failures because the workflow could not access cached results from the original run. The work directory now correctly retains the original value when resuming workflows with different compute environments.
  • Fixed an issue where the settings button in the usage overview widget incorrectly displayed workspace permissions in organization context, and improved workspace settings visibility to dynamically show or hide based on user permissions.
  • Fixed an issue where creator avatars were not displaying in the pipeline version details view due to a missing avatar URL conversion.
  • Fixed an issue where workspace settings buttons displayed incorrectly based on user permissions and context, ensuring the settings button now shows the appropriate organization or workspace settings based on the current view.