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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.

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.

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 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.

MultiQC v1.33

MultiQC

New modules​

  • Seqkit stats (#3401)
    • A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  • RiboTish (#3384)
    • Ribo-seq quality metrics
  • Sylph (#3370)
    • Sylph is a program that performs metagenomic profiling or containment average nucleotide identity querying for metagenomic shotgun sequencing samples.
  • Bbsplit basic stats (#3394)
    • New submodule for bbtools

Feature updates and improvements​

  • Custom logo: dark mode option, custom width option. (#3400)
  • Update Seqera AI chat URL (#3415)
  • Add sample_groups configuration for visual grouping in bar graphs (#3404)
  • Custom content: strip whitespace around categories for tsv,csv (#3421)
  • General Stats: Add configurable help text (#3341)
  • Custom content: support passing help text (#3338)
  • Add new flag "axis_controlled_by_switches" to pconfig that allow control of which axis to apply logarithmic scale (#3423)

Module updates​

  • fastp: Add support for naming samples after --report_title in Fastp command (#3418)
  • Glimpse: Add more decimal to general table stats (#3423)
  • Refactor BISCUIT module for better consistency with current MultiQC codebase (#3345, #3426)
  • Add version fetching for HiCUP, QoRTs, QualiMap, RNA-SeQC (#3420)

Fixes​

  • Fix MultiQC plotly export bug affecting FastQC heatmaps (#3402)
  • Fix bug with sample filter buttons in new template (#3389)
  • Fix KeyError in bargraph when using reference lines with horizontal orientation (#3385)

Module fixes​

  • Fix validation errors in strict mode for invalid plot config options (#3428)
    • Remove invalid hide_zero_cats from line plot configs (mosdepth, bamdst, samtools/coverage, humid, dragen_fastqc)
    • Fix bar plot category configs using invalid fields (picard/IlluminaBasecallingMetrics, motus)
  • Samtools coverage: Don't crash if incorrect number of columns found (#3419)
  • Lima: split delimiter is a tab, not any whitespace. (#3395)
  • Homer: Fix unique / total count swap in homer/tagdirectory (#3381)

Infrastructure and packaging​

  • Avoid Python 3.14.1 (#3414)
  • Version check: Add installation method to detect installs using uv (#3422)
  • Bump pre commit versions (#3417)

Optimization​

  • Make Parquet merging much, much faster (60% faster) (#3403)

New Contributors​

Full Changelog: https://github.com/MultiQC/MultiQC/compare/v1.32...v1.33

Seqera Cloud v25.3.0_cycle34

Seqera Cloud

Feature updates and improvements​

  • Studios
    • Added the ability to configure a custom container repository path for Wave-built Studio images in workspace settings, providing greater control over where container images are stored and distributed.

Bug fixes​

  • Addressed a security vulnerability related to resource allocation, improving overall Platform security.
  • Fixed an issue with interpolated values in dynamic resource labels (e.g., label-name=${workflowId}). Dynamic resource labels now work correctly when the feature is enabled for all workspaces.
  • Fixed an issue with deleted workflows incorrectly counted toward organization quota limits. Active workflow counts now accurately exclude deleted workflows.

Nextflow 25.10.1

Nextflow

Feature updates and improvements​

  • Add default value to Apptainer pull timeout config parameter by @jorgee in #6534
  • Bump logback 1.5.20
  • Bump nf-amazon@3.4.2
  • Bump nf-tower@1.17.2

Bug fixes​

  • Fix asset detection when item is not a sibling of the executed script by @DriesSchaumont in #6605
  • Fix error with dynamic directives with named arguments by @bentsherman in #6550
  • Fix false config validation warnings for process selectors by @bentsherman in #6542
  • Fix Fusion license JWT token refresh by reusing TowerClient by @jorgee in 561ed6c
  • Fix incorrect AWS region when specifying a S3 regional endpoint by @jorgee in #6530
  • Fix issue with optional workflow output by @bentsherman in #6519
  • Fix unordered completed parts in AWS multipart upload by @jorgee in #6560
  • Revert Plugins.init() in run command to original location by @jorgee in #6568

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.1

Nextflow 25.11.0-edge

Nextflow

Feature updates and improvements​

  • Add Google Batch LogsPolicy PATH option for logging to GCS by @dglazer in #6431
  • Add default value to Apptainer pull timeout config parameter by @jorgee in #6534
  • Add test case for printing config with nested includes by @Lehmann-Fabian in #2498
  • Allow pre-existing write-protected plugins directory to be used by @bentsherman in #6594
  • Change log level from warn1 to debug1 for K8s Job Pod Warnings by @BioWilko in #6523
  • Improve error message for invalid accelerator resource by @bentsherman in #6585
  • Improve error message for invalid contribution type in manifest contributors by @bentsherman in #6593
  • Issue templates: add external links via config by @ewels in #6563
  • Move task error formatting logic into separate class by @bentsherman in #6551
  • Optimize exit code handling by relying on scheduler status for successful executions by @jorgee in #6484
  • Remove unnecessary runtime checks with strict syntax by @bentsherman in #6539
  • Remove unused BatchHelper class by @pditommaso in #6547
  • Remove wiremock-groovy dependency and update tests using this dependency by @jorgee in #6611
  • Update bundled Docker runtime to 19.03.15 by @yarikoptic in #6565
  • Update migration timeline for plugin registry by @bentsherman in #6543
  • Update trace table columns in Reports page by @JustinBellavance in #6483
  • Upgrade from Apache Commons Lang 2.6 to Commons Lang3 3.18.0 by @pditommaso in #6511
  • Add admonition to clarify plugin provider and org by @christopher-hakkaart in #6536
  • Add admonition to inputs and index words by @christopher-hakkaart in #6461
  • Improve task previousTrace documentation by @rnaidu in #6538
  • Mark Fusion.tags as supported only for S3 by @fntlnz in #6601
  • Update feature flags page by @christopher-hakkaart in #6504
  • Update task directives by @christopher-hakkaart in #6506
  • Bump Fusion to version 2.5 by @jordeu in #6557
  • Bump Gradle 9.2.0 by @pditommaso in 2657524
  • Bump groovy 4.0.29 by @pditommaso in #6510
  • Bump logback to version 1.5.20 by @pditommaso in 462eec5
  • Bump org.bouncycastle:bcpkix-jdk18on from 1.78.1 to 1.79 by @dependabot in #6537
  • Bump nf-amazon@3.5.0
  • Bump nf-azure@1.21.0
  • Bump nf-google@1.24.0
  • Bump nf-k8s@1.3.0
  • Bump nf-tower@1.18.0
  • Bump nf-wave@1.17.0

Bug fixes​

  • Fix Do not delete K8s jobs when ttlSecondsAfterFinished is set by @bentsherman in #6597
  • Fix Fusion license JWT token refresh by reusing TowerClient by @jorgee in 498125d
  • Fix Invalid type error detection by @pditommaso in 9e3aeed
  • Fix K8sTaskHandlerTest method name typos by @pditommaso in bcf81d9
  • Fix asset detection when item is not a sibling of the executed script by @DriesSchaumont in #6605
  • Fix csv splitter when skipping empty lines by @bentsherman in #6586
  • Fix documentation of unique operator by @bentsherman in #6541
  • Fix error with dynamic directives with named arguments by @bentsherman in #6550
  • Fix false config validation warnings for process selectors by @bentsherman in #6542
  • Fix false error with task ext blocks in strict syntax by @bentsherman in #6569
  • Fix incorrect AWS region when specifying a S3 regional endpoint by @jorgee in #6530
  • Fix invalid cache write when cacheable split operation fails by @bentsherman in #6588
  • Fix issue with optional workflow output by @bentsherman in #6519
  • Fix issues with rsync stage-out mode by @bentsherman in #6587
  • Fix security vulnerabilities in org.json dependency by @pditommaso in c7161c2
  • Fix unordered completed parts in AWS multipart upload by @jorgee in #6560
  • Fix TowerJsonGenerator thread-safety issue by @pditommaso in #6619
  • Fix Plugins.init() in run command to original location by @jorgee in #6568
  • Fix security vulnerabilities for wiremock by @jorgee in #6607
  • Fix replace complete plotly bundle with smaller more specific one by @mashehu in #6527
  • Fix stageFileEnabled flag to control .command.stage file creation by @pditommaso in #6618

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.11.0-edge

Wave v1.30.0

Wave

Feature updates and improvements​

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

Bug fixes​

  • Fixed typos in Wave Kubernetes install by @christopher-hakkaart in #930
  • Fixed scan and mirror enabled flag bug by @munishchouhan in #935
  • Fixed 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_cycle33

Seqera Cloud

Feature updates and improvements​

  • Studios
    • Updated the Add Studio page to a single-step form.
  • AWS Batch compute environments now use AmazonLinux2023-based AMIs by default, offering improved security (IMDSv2), better performance with gp3 EBS volumes, and a more recent kernel. Existing compute environments continue to function with AmazonLinux2 without changes, though we recommend migrating to newer compute environments before AmazonLinux2 reaches end-of-life in June 2026.

Bug fixes​

  • Fixed compute environment variables created without specifying a target environment (head or compute), which resulted in variables not being applied during workflow execution. The system now validates that at least one target environment is specified, preventing invalid configurations and providing clear error messages.
  • Fixed display issues with long helper text in pipeline schema forms. Helper text now wraps properly within form controls, improving readability for parameter descriptions with technical specifications or long value lists.