Changelog: MultiQC

The MultiQC v1.32 release features one major change:

• Bootstrap upgrade and DARK MODE (#3264)

This has been brewing for a long time, and is a large rewrite of how MultiQC HTML / CSS and JS is written and packaged.

MultiQC now supports simple theming with Bootstrap color modes, and the updated default template ships with both light- and dark-mode by default 😎.

The old template is still available, but has been renamed to original.

Adding new module for Xenium analysis, 10x Genomics Xenium spatial transcriptomics quality control report.

The parquet format is stable since 1.29, renaming the output file from BETA-multiqc.parquet to multiqc.parquet.

JSON schema for MultiQC config & AI summaries fixes and optimizations.

Fixes and improvements in AI summaries:​

• AI summaries should now work with bioconda install multiqc without additional dependencies
• Supporting other LLM providers with a custom endpoint passed through the command line (docs)
• Option to anonymize sample names

Christmas release! 10 new modules, 11 improved modules, and a few core improvements.

Multiple bug fixes and minor updates.

Python 3.13, bugs fixed, improved sample grouping UI, and handling freezes in containers with incompatible architectures.