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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.

Nextflow 25.12.0-edge

Feature updates and improvements​

Language features​

  • Added listDirectory() to Path type and deprecate listFiles() by @bentsherman in #6581
  • Set local task exit status when time limit is exceeded by @bentsherman in #6592

Google Batch​

  • Added default maxSpotAttempts for Fusion Snapshots in Google Batch by @fntlnz in #6652
  • Refactored Google Batch getExitCode to imperative style by @pditommaso in #6649

Kubernetes​

  • Added runtimeClassName to the pod options by @alexpilotti in #6633

Wave​

  • Added wave.build.template config option by @pditommaso in #6639

Plugins​

  • Added README files for all plugins by @pditommaso in #6660
  • Checked Nextflow version before loading plugins by @bentsherman in #6591

General​

  • Added onlyJobState option for SLURM executor by @tcutts in #6659
  • Added Spot interruption tracking to trace records by @munishchouhan in #6606
  • Added URL encoding when revision name is used as HTTP query parameter by @jorgee in #6598
  • Added warnings to JSON output in lint command by @ewels in #6625
  • Implemented Git multiple revisions by @jorgee in #6620
  • Added Nextflow Development Constitution by @pditommaso in #6578
  • Added extra warnings as 25.10 is added to Platform by @christopher-hakkaart in #6655
  • Added longer NXF_SYNTAX_PARSER descriptions by @christopher-hakkaart in #6637
  • Documented best practices for script and config params by @bentsherman in #6631
  • Fixed typos by @christopher-hakkaart in #6641
  • Improved preview feature warnings in documentation by @pditommaso in #6663
  • Updated note about AWS CLI by @christopher-hakkaart in #6626
  • Updated NXF_SYNTAX_PARSER callouts by @christopher-hakkaart in #6640

Bug fixes​

Language features​

  • Fixed optional param in params block by @bentsherman in #6657
  • Fixed validation of numeric types in params block by @bentsherman in #6656

Wave​

  • Fixed WaveClient sending Bearer token to public S3 URLs by @pditommaso in #6672

Plugins​

  • Fixed String.format error when plugin URL contains percent chars by @pditommaso in #6651

General​

  • Fixed GitHub repository provider when providing token with auth property by @jorgee in #6662
  • Fixed tolerate spaces in $NXF_TASK_WORKDIR by @TheLostLambda in #6421

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.12.0-edge

Fusion v2.5.8

How to pin this version​

fusion {
  enabled = true
  containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.8-amd64.json'
}
info

For ARM64 CPU architecture, use containerConfigUrl = 'https://fusionfs.seqera.io/releases/v2.5.8-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 with a 5-minute timer.

GPU​

  • GPU tracer improvements: Consistent logging, --no-color flag support, and enabled by default in containers.

Bug fixes​

General​

  • Race condition fix: Prevented data loss from concurrent Unlink() and Mknod() operations on the same path.

Upgrade notes​

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

Seqera Enterprise v25.3.1

info

The legacy distribution endpoint at cr.seqera.io/private is deprecated. Only bug fixes for existing major releases will continue to be published there. New major releases of Seqera Platform are available from cr.seqera.io/enterprise. Seqera will provide updated credentials for the new endpoint — contact your Seqera representative if you need access.

Bug fixes​

Compute environments​

  • Resolved an issue with long-running jobs and sts caching.

Nextflow​

Nextflow upgraded to 25.10.2​

Seqera Platform 25.3.1 includes Nextflow 25.10.2 (previously 25.04.8).

According to the 25.10.0, 25.10.1, and 25.10.2 release notes, there are breaking changes for AWS configurations and the deprecated Google Life Sciences executor. However, existing pipelines will continue to work. New recommended syntax is now available:

New features:

  • Workflow params: New params block for declaring pipeline parameters with type annotations (requires strict syntax)
  • Workflow outputs out of preview: Workflow outputs are now production-ready (remove nextflow.preview.output flag if using)
  • Type annotations: Support for type annotations on parameters, workflows, processes, and functions (requires strict syntax)
  • Auth and Launch commands: New nextflow auth and nextflow launch commands for Seqera Platform integration

Enhancements:

  • Nextflow plugin registry for more efficient plugin downloads
  • Simpler syntax for workflow handlers (onComplete, onError sections in workflows)
  • Simpler syntax for dynamic directives (no closure required with strict syntax)
  • Configurable date formatting via NXF_DATE_FORMAT environment variable

Breaking changes:

  • google-lifesciences executor removed (use google-batch instead)
  • AWS Java SDK upgraded from v1 to v2 (affects aws.client config options)
  • Package nextflow.config.schema renamed to nextflow.config.spec

See the Nextflow 25.10 migration guide for full details.

Note: The default Nextflow version can be overridden by setting NXF_VER in a pre-run script:

export NXF_VER=25.04.8

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.

Seqera Enterprise v25.3

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.

info

The legacy distribution endpoint at cr.seqera.io/private is deprecated. Only bug fixes for existing major releases will continue to be published there. New major releases of Seqera Platform are available from cr.seqera.io/enterprise. Seqera will provide updated credentials for the new endpoint — contact your Seqera representative if you need access.

Feature updates 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.

General​

  • 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 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​

Studios​

  • Fixed Studios AWS cloud private ECR pull issues.
  • Fixed handling of Studios tokens without user ID claim.
  • Fixed trigger YAML validation on Studios config patch.

Pipelines​

  • Fixed pipeline list not updating when changing workspace.
  • Fixed pipeline config reading from same directory as main script.
  • Fixed describePipeline to properly handle avatar files.

Workflows​

  • Prevented incorrect workdir patching when resuming workflow with compute environment changes.
  • Added proper permission checks for workflow star functionality.

Compute environments​

  • Fixed transactional event listener annotation for compute operations.
  • Improved Connect parameter handling for compute environments.
  • Fixed error when saving long container names.

UI/UX​

  • Fixed MultiQC plots displaying as grey boxes.
  • Fixed badge cropping issues in Platform UI.
  • Fixed infinite scroll in optimization profile modal.
  • Forced perfect circle avatar shape for consistent rendering.

Permissions and roles​

  • Removed blanket ListOrganizationSettings check, use individual permissions instead.

General​

  • Fixed OIDC API handling in authentication flows.

Fusion​

See the Fusion changelog for more details.

Wave​

See the Wave changelog for more details.

Nextflow​

Nextflow upgraded to 25.04.8​

Seqera Platform 25.3 includes Nextflow 25.04.8 (previously 25.04.3 from v25.2).

According to the 25.04.0 through 25.04.8 release notes, this update includes bug fixes and stability improvements. Existing pipelines will continue to work.

See the Nextflow 25.04 migration guide for full details.

Note: The default Nextflow version can be overridden by setting NXF_VER in a pre-run script:

export NXF_VER=25.04.x

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.

MultiQC​

See the MultiQC changelog for details.

General warnings​

Starting in version 26.1, the root user image is deprecated. We recommend switching to the unprivileged (rootless) image during this upgrade. To do so:

  • Update the image tag.
  • Modify your Kubernetes Service resource or Docker Compose service definition to forward requests to port 8000 (the default for the unprivileged image).

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.