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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

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.

Nextflow 26.04.0

Nextflow 26.04 is a stable release

See the Migrating to 26.04 for a comprehensive list of changes since the last stable release.

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

Wave v1.33.3

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

Seqera Enterprise v25.3.6

Feature updates and improvements​

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.

Access control​

  • Added PKCE and consent flow support to OIDC, enabling Seqera Platform to act as an identity provider for OIDC/OAuth2 clients such as the Seqera AI CLI.

Bug fixes​

Pipelines​

  • Fixed Nextflow timeline config generation to resolve NXF_TML_FILE via System.getenv instead of relying on shell variable expansion.
  • Fixed the Browse button in the pipeline launch form being hidden for users with Launch, Connect, or View workspace roles by gating it on the correct permission instead of the Studios studio:execute grant.

Upgrade notes​

No breaking changes. Standard upgrade procedure applies.