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​

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​

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

Feature updates and improvements​

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.

Feature updates and improvements​

Language features​

• Removed unnecessary runtime checks with strict syntax by @bentsherman in #6539

Dependencies​

• Bumped nf-amazon@3.4.4
• Bumped nf-google@1.23.5
• Bumped nf-tower@1.17.5

Bug fixes​

Language features​

• Fixed false error with optional param by @bentsherman in #6811
• Fixed false error with multi-line tuple assignment in v2 parser by @bentsherman in #6786
• Fixed false error in v2 parser when including config file from HTTP URL by @bentsherman in #6753

AWS Batch​

• Added isCompleted check in getNumSpotInterruptions by @munishchouhan in #6806

General​

• Fixed LogsCheckpoint thread blocking shutdown for up to 90 seconds by @pditommaso in #6787

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.03.4-edge

New modules​

• Methurator (#3447)
  • A Python package designed to estimate CpGs saturation for DNA methylation sequencing data.
• riboWaltz (#3465)
  • Computes P-site offsets and performs quality control for ribosome profiling (Ribo-seq) data.

Feature updates and improvements​

• Add uv as an installation method in docs and README (#3493)
• Add Claude PostToolUse hook for code formatting (#3461)
• Bump default AI models for Anthropic (#3430)
• Remove HTML tags in generated module docs (#3509)
• Enable code review workflow to post comments on PRs (#3506)
• better header k/v spacing (#3471)
• Hide AI summary sections when simple_output is enabled (#3500)
• export_plots_timeout: Add docs and increase default to 60s (#3433)

Module updates​

• Clarify RSeQC bam_stat proper pairs column title (#3526)
• Fix mosdepth coverage in general stats if key is missing (#3432)
• fastp: Add limits, update color scale of % PF/% Adapter (#3454)
• fastp: Pick up version number for fasterp runs (#3392)
• Freyja: Use safe alternative to eval() (#3531)

Fixes​

• Fix heatmap axis labels not updating when toggling clustering (#3487)
• Fix bug: Toggling highlighting for AI summary sample names didn't work (#3455)
• fix table scroll styling with sticky headers (#3437)

Module fixes​

• Fix sample name cleaning in CheckM and CheckM2 modules (#3464)
• CrosscheckFingerprints: Fix bug due to overwriting row_number variable (#3458)
• Porechop: Fix bug with "End Trimmed Percent" denominator (#3456)
• Fix incorrect plot title in umicollapse module (#3446)
• SNPsplit: Fix module datetime serialization error (#3444)

Infrastructure and packaging​

• Switch from pre-commit to prek (#3467)

New Contributors​

• @CelinePrakash made their first contribution in https://github.com/MultiQC/MultiQC/pull/3458
• @nictru made their first contribution in https://github.com/MultiQC/MultiQC/pull/3487
• @drbh made their first contribution in https://github.com/MultiQC/MultiQC/pull/3392

Full Changelog: https://github.com/MultiQC/MultiQC/compare/v1.33...v1.34

Feature updates and improvements​

Language features​

• Added option to disable printing workflow outputs by @bentsherman in #7018
• Resolved structured process input types by @bentsherman in #7014

S3​

• Applied socket timeout to S3 CRT connections by @jorgee in #7024
• Managed AWS SDK exceptions to convert to the appropriate IO exceptions by @jorgee in #6707

Plugins​

• Updated missing pf4j updates by @jorgee in #7016

Fusion​

• Added Fusion GPU metrics collection by @pditommaso in #7022
• Used Fusion trace metrics to replace bash command-trace wrapper by @pditommaso in #7041

General​

• Added -files-from option to lint command to avoid ARG_MAX limit by @adamrtalbot in #6858
• Added 26.04 migration docs by @bentsherman in #7000
• Allowed cloning from local Git repositories when --offline by @MatthiasZepper in #7035
• Allowed running pipeline from URL and main script path by @jorgee in #6602
• Filtered autoLabels to selected workflow-metadata fields by @pditommaso in #7049
• Honored process.resourceLabels in nf-seqera executor by @pditommaso in #7048
• Renamed module info subcommand to module view by @pditommaso in #7052
• Simplified demo module README template by @pditommaso in #7051
• Suppressed lint progress logging with -q flag by @ewels in #6880

Bug fixes​

Language features​

• Fixed formatting issues with complex expressions by @bentsherman in #7027

S3​

• Fixed S3FileSystemProvider.newInputStream() draining full object on close by @jorgee in #7046

Plugins​

• Fixed inconsistent indentation in nf-amazon by @bentsherman in #7047
• Fixed nextflowVersion for nf-tower and nf-seqera plugins by @pditommaso in cbc0a2d8e

General​

• Fixed generated process name in module create command by @jorgee in #7008
• Fixed module info formatting separator by @pditommaso in #7033
• Fixed resolution of -with-tower with TOWER_API_ENDPOINT by @bentsherman in #7045
• Fixed saveCacheFiles early return skipping log file uploads by @munishchouhan in #7015

Dependencies​

• Bumped org.bouncycastle:bcpkix-jdk18on from 1.79 to 1.84 by @dependabot in #7042
• Bumped nf-amazon@3.8.3
• Bumped nf-k8s@1.5.2
• Bumped nf-seqera@0.18.0
• Bumped nf-tower@1.25.0
• Bumped nf-wave@1.19.1

Full changelog: https://github.com/nextflow-io/nextflow/releases/tag/v26.03.3-edge