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Seqera Cloud v26.1.0_cycle55

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.

MultiQC v1.35

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 ✨

CleanShot 2026-05-13 at 02 56 00@2x

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​

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

Nextflow 26.04.1

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

Seqera Cloud v26.1.0_cycle54

note

The default Nextflow version has changed from v25.10 to v26.04. Nextflow v26.04 includes the strict syntax as default, which may break some older workflows. See Enable Nextflow syntax parser v2.

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.

Nextflow 25.10.5

Nextflow 25.10 is a stable release

See the Migrating to 25.10 for a comprehensive list of changes since the last stable release.

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

Seqera Cloud v26.1.0_cycle52

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.

Seqera Cloud v26.1.0_cycle53

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.