Happy to say MultiQC v1.35 is out 🎉
The headline feature: a MultiQC Config Wizard 🧙♂️
If you've ever sat down to write a MultiQC config from scratch, you'll know there are a lot of options to wade through (around 150 of them). The wizard gives you a browsable form for every single one, with help text, examples, and live validation as you type. You can also paste in an existing YAML config and have it explained, checked, and fixed up.
Video below 👇
The Config Wizard is a static HTML page that ships with MultiQC, but the easiest way to try it is online (no signup, no install):
The Pydantic model that powers the config is also used to autogenerate comprehensive new documentation, and a JSON schema that goes to schemastore.org. This means if you save a 'multiqc_config.yaml' file in #VSCode you'll get native inline validation 🚀
Also in v1.35: eight new modules 🧩
• CheckAtlas: QC for single-cell atlases
• Deacon: fast host depletion for FASTA/FASTQ
• FastQE: FASTQ quality scores as emoji 🤓
• hicstuff: Hi-C contact map generation
• HiFi-Trimmer: PacBio HiFi adapter trimming
• Riker: Rust port of Picard QC tools
• sincei: single-cell (epi)genomics toolkit
• Trim Galore: native v2.x support!
🛠 Bigger module updates for Bases2Fastq (major overhaul), Falco (now auto-detected), Fastp (% surviving bases), and Sequali (expanded stats + normalised plots).
✨ Plus section alerts for filtered samples, per-tab plot configs, custom favicons, and a defaultsort fix for the first table column.
🐛 Fixes for Bcftools, Cell Ranger ARC, Dragen FastQC, Haplocheck, empty plot zip exports, and env vars being stored as strings.
🔧 Minimum Python is now 3.9, plus easier Polars build deps.
Full release notes here: 👉 https://github.com/MultiQC/MultiQC/releases/tag/v1.35
Huge thanks to everyone who sent in PRs and bug reports for this release ❤️
MultiQC
