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Seqera Cloud v26.1.0_cycle56

Feature updates and improvements​

Compute environments​

  • Added a configurable boot disk size for Azure Batch pools.
  • Added r8idn, r8idb, m8idn, and m8idb instance families to the NVMe list.

Monitoring​

  • Improved the JSON diff component with small refinements.

Pipelines​

  • Added the Lineage ID to the Run Info page.

General​

  • Introduced a panel search input and integrated it into the navigation switcher component.
  • Improved workspace switch redirects to preserve the active sidebar section.

Bug fixes​

Access control​

  • Fixed the audit event type for MANUAL-to-SCIM promotion.
  • Kept the infinite-scroll drop-down open when clicking the search input.

Compute environments​

  • Improved Entra robustness by adding equals/hashCode for credentials and making the managed identity regex case-insensitive.
  • Deduplicated the compute environment entry in the launch drop-down.

Data Explorer​

  • Made credentials a required field in the Add data repository form.
  • Fixed the Data Explorer custom bucket E2E test to select credentials.

Monitoring​

  • Fixed a referential integrity constraint violation when saving an audit log image bundle in H2.
  • Replaced the word ID with IP in the audit logs table.
  • Coalesced setAvailableCredits calls per organization.
  • Coalesced stop events per organization using a Redis lock.
  • Added a differential TTL and empty-result guard for the Metronome balance cache.
  • Coalesced handleOrganizationCreditsExpiration calls per organization.
  • Skipped null balance puts in listGrantBalance to avoid a ConcurrentHashMap NPE.

Pipelines​

  • Refined workflow_updated events that contain no diff.
  • Prevented duplicate GitHub credentials across PAT and GitHub App types.
  • Resolved file paths to the most recent lineage record.

General​

  • Fixed the expandable-text overlay to display only when text is truncated.
  • Preserved panel search focus inside mat-menu.

Nextflow 26.04.2

Feature updates and improvements​

Language features​

  • Validated module spec against JSON schema by @pditommaso in #7094
  • Updated guidelines for strict parser by @bentsherman in #7134

General​

  • Honored token field in BitbucketServerRepositoryProvider by @jorgee in #7120
  • Picked up force-pushed branches in multi-revision repo strategy by @jorgee in #7103
  • Tightened CI security and removed dead code in workflows by @ewels in #7139
  • Updated GitHub Actions with security updates by @ewels in #7138

Dependencies​

  • Pinned python to 3.14.5 by @seqeralabs-renovate in #7152
  • Bumped nf-azure@1.22.4 by @pditommaso in 2bcc6e8c
  • Bumped nf-k8s@1.5.3 by @pditommaso in b2ea7492
  • Bumped nf-seqera@0.20.0 by @pditommaso in 4d55e81e

Bug fixes​

Language features​

  • Fixed module run to allow optional path inputs by @bentsherman in #7163
  • Fixed destructured record input in module run by @bentsherman in #7164
  • Fixed function calls in typed process outputs by @bentsherman in #7148
  • Fixed strict parser to include params refs in task hash by @bentsherman in #7165
  • Normalized TaskPath to Path in typed process outputs by @stekaz in #7090

Azure​

  • Fixed Azure rnaseq-nf test by @bentsherman in #7143

General​

  • Released HTTP sockets when reading HTTP attributes to avoid 503 throttling by @jorgee in f2b0284e

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.04.2

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