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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

MultiQC v1.32

MultiQC

The MultiQC v1.32 release features one major change:

  • Bootstrap upgrade and DARK MODE (#3264)

This has been brewing for a long time, and is a large rewrite of how MultiQC HTML / CSS and JS is written and packaged.

MultiQC now supports simple theming with Bootstrap color modes, and the updated default template ships with both light- and dark-mode by default 😎.

The old template is still available, but has been renamed to original.

Seqera Cloud v25.3.0_cycle28

Seqera Cloud

General updates and improvements​

  • Seqera Compute
  • Platform
    • Added a copy button to data display chips, allowing you to quickly copy displayed values to your clipboard.
    • Added an improved onboarding flow for Seqera Compute customers to quickly run pipelines.
  • Pipelines
    • Added support for pinning the HEAD commit ID of the chosen revision to guarantee deterministic pipeline execution.
  • Data Explorer
    • Added support for image preview and file upload in Data Explorer when using Amazon S3-compatible API storage (for example, but not limited to, Cloudflare R2, MinIO, and Oracle Cloud).
    • Added support for MinIO object storage in Data Explorer, enabling users to browse, upload, and download files from MinIO instances using S3-compatible credentials.
  • Added the ability to read task logs on Azure Cloud from Azure Blob Storage after pipeline completion, ensuring logs remain accessible throughout the entire task lifecycle.
  • Updated the nf-launcher container versions from 25.04.6 to 25.04.8 for both standard and Docker-in-Docker variants.
  • Updated the default Seqera AMI version to 0.0.10 for both AMD64 and ARM64 architectures in AWS Cloud deployments.

Bug fixes​

  • Fixed an issue where resuming pipelines failed due to incorrect identification of launchable entity types.
  • Fixed issues where version name autogeneration used incorrect defaults and navigation returned users to the wrong page when editing pipeline versions.
  • Fixed an issue where users with Launch permissions could not access Studios due to insufficient workspace settings permissions.
  • Fixed an issue where administrators could accidentally create duplicate user accounts due to differences in email address casing.