Feature updates and improvements​

Compute environments​

• Added a CloudInfo cloud instance type catalog and chip-selector filters specification.
• Added a description field to the Compute Environment V2 form.

Datasets​

• Exposed dataset file size in version API responses.

Monitoring​

• Added a getCost failure metric.
• Rendered fractional Allocated CPU values on the Run Details metrics card.
• Added SCIM group audit logs.

Pipelines​

• Added a Nextflow syntax parser v2 toggle.
• Added launch-time settings to the workflow configuration tab.

Studios​

• Added the compute environment name to the Studios row card.
• Added new API endpoints to fetch compatible compute environments for a Studio and update the compute environment on a Studio.
• Enabled updating the compute environment on a Studio.
• Resolved the user on SSH Studio connection attempts.

Data Explorer​

• Cached the impersonated signer for WIF pre-signed URLs.

General​

• Introduced scroll-into-error behavior for the notification container component and unified the placement of message containers across form pages.
• Collapsed Settings breadcrumbs to two segments.
• Refined styling for the bordered variant of label values.
• Improved readability of usage chip icons on dark backgrounds.

Bug fixes​

Access control​

• Redirected on JWT expiry and stopped the onboarding polling loop.
• Auto-created organization membership during IdP group reconciliation.
• Polished the IdP group mapping UI.

Compute environments​

• Validated NVMe and Wave dependencies for Fusion v2.
• Split Forge disposal into separate resources and credentials phases.
• Ported the Forge disposal split to Azure and GCP.
• Clarified setRemoteAvailableCredits behavior and floored stale balance updates.
• Granted lineage store access to the forged AWS Batch role.
• Bumped the GCP default GPU image family to CUDA 12.9.
• Resolved the WIF credential owner context inside a read-only transaction.

Data Explorer​

• Supported GCS pre-signed URLs with WIF credentials in Data Explorer.

Pipelines​

• Disabled the lineage launch toggle when lineage settings are not configured or when the compute environment does not support lineage.
• Set the default value for Launch.syntaxParser to match the database schema.
• De-flaked the PipelineServiceTest agent revisions check.

Studios​

• Recovered legacy Studio event names in the usage query.
• Fell back to baseline Studio capabilities when the manifest is missing or the Studio version is not found in the manifest.

General​

• Pinned the Netty allocator to pooled to mitigate Micronaut 4.9 direct memory growth.
• Stopped ProviderUnrecoverableException from hiding JVM errors.
• Increased the polling timeout for the async audit image bundle test.

This release has a very nice shiny new feature for you: the MultiQC Configuration Wizard! 👨🏻‍🎨 🎨

This has an interactive form where you can browse all MultiQC config attributes (there are quite a lot). See them organised with help text and examples. Enter values into the form and have them validated in real time. 📋 ✅

Then see your generated YAML config in a code editor (where you can paste existing configs if you wish). See the config file explained, validated and suggestions for fixes. 📚

The config wizard is a static HTML file that is bundled with the MultiQC repo, but it's easiest to try out online: https://seqera.io/multiqc_config_wizard ✨

New modules​

• CheckAtlas (#3545)
  • A one-liner tool for quality control of single-cell atlases.
• Deacon (#3564)
  • Search and depletion of FASTA/FASTQ files and streams using accelerated minimizer matching.
• FastQE (#3490)
  • Uses emoji to represent FASTQ sequence quality scores.
• hicstuff (#3541)
  • Hi-C pipeline that generates contact maps from sequencing reads.
• HiFi-Trimmer (#3513)
  • Filters and trims adapter sequences from HiFi reads using BLAST.
• Riker (#3540)
  • Fast Rust toolkit that ports key sequencing QC tools from Picard.
• sincei (#1946)
  • Toolkit for processing and analysing single-cell (epi)genomics data.
• Trim Galore (#3538)
  • Native v2.x support: quality and adapter trimming for next-generation sequencing data, with special handling for RRBS libraries.

Module updates​

• Bases2Fastq: Major upgrade to the module, now shows a lot more information (#3460)
• Falco: Add native recognition for Falco output (#3497)
• Fastp: Add % surviving bases (#3472)
• Sequali: Expand general statistics, add normalised plots (#3530)

Module fixes​

• Bcftools: Fix stats zero-depth plot crash (#3556)
• Cell Ranger ARC: Fix key collisions between ATAC and GEX metrics (#3480)
• Dragen: Fix incorrect average GC% in FastQC for all samples except the first in batch (#3505)
• Haplocheck: Don't overwrite prior results, allow multiple samples (#3512)

Feature updates and improvements​

• Config: Major new automations using config schema (#3183, #3558, #3561)
  • Automated markdown reference documentation of all config attributes for the docs
  • New interactive tool for building, editing and validating MultiQC config files: https://seqera.io/multiqc_config_wizard
• AI: Catch unexpected AWS Bedrock response shapes (#3440)
• custom_plot_config: Fix deprecated camelCase aliases (e.g. yPlotBands) (#3547)
• custom_plot_config: Per-tab targeting for multi-data_labels plots (#3548)
• Custom content: Fix crash on data type conflict between files (#3560)
• Custom images: Support more MIME types, add custom favicon (#3469)
• Plots: Add section alerts for filtered samples (#3549)
• Plots: Fix barplot ValueError when all categories are zero (#3563)
• Report: Add spacing between AI summary and general stats (#3470)
• Run merging: Fix grouped sample totals and hierarchy being lost during parquet merging (#3559)
• Tables: Allow defaultsort to include the first column header (#3519)
• Tests: Fix pytest warning sources (#3551)

Fixes​

• Config: Fix env var overwrite where booleans/ints/floats were stored as strings (#3557)
• Core: Fix rich.panel import in module-failure exception handler (#3537)
• custom_plot_config: Fix parsing of y_bands/x_bands/x_lines/y_lines (#3459)
• Report: Fix race causing empty zip files when exporting plots (#3555)

Infrastructure and packaging​

• Claude Code: Update agent instructions (#3552)
• Frontend: Update npm packages (#3562)
• Packaging: Bump minimum Python to 3.9 (#3542)
• Polars: Replace deprecated polars-lts-cpu dependency (#3553)
• Polars: Use Pyodide-compatible dependency on Emscripten (#3554)

Optimization, refactoring and typing​

• Linting: Drop Python 2-era idioms (#3546)

New Contributors​

• @hemant-goyal made their first contribution in https://github.com/MultiQC/MultiQC/pull/3497
• @FelixKrueger made their first contribution in https://github.com/MultiQC/MultiQC/pull/3538
• @yunhailuo made their first contribution in https://github.com/MultiQC/MultiQC/pull/3480
• @vivekbhr made their first contribution in https://github.com/MultiQC/MultiQC/pull/1946
• @tfenne made their first contribution in https://github.com/MultiQC/MultiQC/pull/3540
• @muffato made their first contribution in https://github.com/MultiQC/MultiQC/pull/3513
• @js2264 made their first contribution in https://github.com/MultiQC/MultiQC/pull/3541
• @chelauk made their first contribution in https://github.com/MultiQC/MultiQC/pull/3492

Full Changelog: https://github.com/MultiQC/MultiQC/compare/v1.34...v1.35

Feature updates and improvements​

General​

• Updated migration docs now that 26.04 is released by @ewels in #7085

Dependencies​

• Bumped ch.qos.logback:logback-classic to v1.5.32 by @seqeralabs-renovate in #7126
• Bumped nf-amazon@3.9.1 by @pditommaso in 816c0774
• Bumped nf-azure@1.22.3 by @pditommaso in 78fa5013
• Bumped nf-codecommit@0.5.2 by @pditommaso in 4ae5c872
• Bumped nf-seqera@0.19.1 by @pditommaso in 764003a9

Bug fixes​

General​

• Fixed module binaries on nextflow module run via session flag by @pditommaso in #7089

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.1

Feature updates and improvements​

General​

• Truncated verbose DEBUG log payloads to reduce heap pressure by @pditommaso in #1041

Full changelog: https://github.com/seqeralabs/wave/compare/v1.33.3...v1.33.4

Feature updates and improvements​

Access control​

• Automatically disabled SSO on organization deletion.
• Enabled SSO domain verification.
• Skipped showcase workspace enrollment for free-tier users.

Compute environments​

• Added an export configuration option to the compute environment menu.

General​

• Added inactive scope styles and a settings breadcrumb trail.
• Aligned workspace settings routes and page titles.
• Updated workspace settings hub copy and added E2E selectors.
• Updated the labels page and modal type copy.

Bug fixes​

Compute environments​

• Fixed the compute environment edit form to skip name copy-rename when opened.

Data Explorer​

• Prevented bucket actions from becoming stuck in the CREATING state.

Studios​

• Fixed the redirection route for the Save as new Studio action.

Feature updates and improvements​

Dependencies​

• Bumped nf-tower@1.17.6 by @pditommaso

Bug fixes​

Language features​

• Fixed formatting bug with map key expression by @bentsherman in #6893
• Fixed incorrect evaluation of secret process directive by @bentsherman in #6934
• Fixed params block in included module by @bentsherman in #6940
• Fixed params inclusion across modules in v2 parser by @bentsherman in #6766

Configuration​

• Fixed resolution of params in resolved config text by @jorgee in #7072

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v25.10.5

Feature updates and improvements​

Compute environments​

• Added force-delete for stuck compute environments.
• Added an optional description field to compute environments.
• Added region name search to the Seqera Compute drop-down mwnu.

Pipelines​

• Added Nextflow lineage integration with indexing, API, and UI for browsing workflow lineage data.
• Added cron action source for scheduled pipeline launches.
• Added effectiveCpus and effectiveMemory helpers on Task.

Monitoring​

• Added GPU metrics.

General​

• Added automatic breadcrumb navigation in the page header.

Bug fixes​

Compute environments​

• Fixed AWS Batch child jobs to terminate on workflow cancellation.
• Added hpc6id to the NVMe instance families allowlist.

Data Explorer​

• Fixed 403 errors to surface properly when adding a data-link to a GCS bucket.
• Fixed text overflow in the Data Explorer modal.

Pipelines​

• Fixed cpuShares to vCPU conversion in Task.getEffectiveCpus.
• Fixed parameters being hidden in the launch form when hidden=false is set in nextflow_schema.json.

Access control​

• Fixed user metadata reading for name, surname, and organization fields.
• Fixed organization claim reading to use the namespaced claim instead of user_metadata.
• Classified DCR-registered OIDC clients as third-party.
• Updated the default refresh token expiration in OIDC.
• Fixed POST /metering to allow regular authenticated users.

Studios​

• Fixed the Studio form to enable buttons after valid input.
• Fixed the Mount data button to display on the Studios form.

General​

• Fixed copy icon position by pinning it to the top-right corner in code blocks.

Feature updates and improvements​

Access control​

• Added an Enterprise AI OAuth client parameter.
• Added the ability to edit workspaces from the admin panel.
• Added configurable access and refresh token expiration per client.
• Refined the copy in the SSO management section.

Compute environments​

• Added a compute instance types selector for AWS Cloud Scheduler.
• Aggregated CPU-hours in shares to preserve fractional allocations.

Pipelines​

• Added data lineage indexing.
• Enabled the AI debug button.

Platform API​

• Persisted requested CPU and memory values on WorkflowLoad.

Bug fixes​

Access control​

• Fixed frontend Cloud SSO feature handling.
• Updated the default refresh token expiration in OIDC.

Datasets​

• Fixed the dataset name maximum length in the frontend to match the backend.

Pipelines​

• Resolved a race condition in the Lineage section of task details.

Feature updates and improvements​

Configuration​

• Renamed nextflow.preview.types feature flag to nextflow.enable.types by @pditommaso in #7067
• Added support for validation of collection params with record types by @bentsherman in #7025

General​

• Added -user-secret and -workspace-secret flags to nextflow launch by @rnaidu-seqera in #7040

Bug fixes​

Language features​

• Fixed runtime type reflection in nf-lang by @bentsherman in #7077

General​

• Fixed ANSI colors in error messages by @ewels in #7078

Dependencies​

• Bumped nf-tower@1.27.0

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.0

Feature updates and improvements​

Container building​

• Added BuildEnabled flag in MultiPlatformBuildService by @munishchouhan in #1030

General​

• Added missing configuration documentation by @munishchouhan in #1025
• Refined Docker Compose setup for Wave Lite by @munishchouhan in #1033
• Reduced Wave resource requirements in installation manifests by @bebosudo in #1028
• Updated documentation with minor clarity improvements by @christopher-hakkaart in #1034

Dependencies​

• Updated third-party dependency versions to latest stable by @cristianrcv in #1037

Bug fixes​

Container building​

• Added micromamba clean to v2 templates to reduce image size by @munishchouhan in #1038

Singularity​

• Fixed pixi Singularity template PATH environment by @munishchouhan in #1036

Full changelog: https://github.com/seqeralabs/wave/compare/v1.33.2...v1.33.3