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MultiQC v1.34

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​

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

MultiQC v1.33

New modules​

  • Seqkit stats (#3401)
    • A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  • RiboTish (#3384)
    • Ribo-seq quality metrics
  • Sylph (#3370)
    • Sylph is a program that performs metagenomic profiling or containment average nucleotide identity querying for metagenomic shotgun sequencing samples.
  • Bbsplit basic stats (#3394)
    • New submodule for bbtools

Feature updates and improvements​

  • Custom logo: dark mode option, custom width option. (#3400)
  • Update Seqera AI chat URL (#3415)
  • Add sample_groups configuration for visual grouping in bar graphs (#3404)
  • Custom content: strip whitespace around categories for tsv,csv (#3421)
  • General Stats: Add configurable help text (#3341)
  • Custom content: support passing help text (#3338)
  • Add new flag "axis_controlled_by_switches" to pconfig that allow control of which axis to apply logarithmic scale (#3423)

Module updates​

  • fastp: Add support for naming samples after --report_title in Fastp command (#3418)
  • Glimpse: Add more decimal to general table stats (#3423)
  • Refactor BISCUIT module for better consistency with current MultiQC codebase (#3345, #3426)
  • Add version fetching for HiCUP, QoRTs, QualiMap, RNA-SeQC (#3420)

Fixes​

  • Fix MultiQC plotly export bug affecting FastQC heatmaps (#3402)
  • Fix bug with sample filter buttons in new template (#3389)
  • Fix KeyError in bargraph when using reference lines with horizontal orientation (#3385)

Module fixes​

  • Fix validation errors in strict mode for invalid plot config options (#3428)
    • Remove invalid hide_zero_cats from line plot configs (mosdepth, bamdst, samtools/coverage, humid, dragen_fastqc)
    • Fix bar plot category configs using invalid fields (picard/IlluminaBasecallingMetrics, motus)
  • Samtools coverage: Don't crash if incorrect number of columns found (#3419)
  • Lima: split delimiter is a tab, not any whitespace. (#3395)
  • Homer: Fix unique / total count swap in homer/tagdirectory (#3381)

Infrastructure and packaging​

  • Avoid Python 3.14.1 (#3414)
  • Version check: Add installation method to detect installs using uv (#3422)
  • Bump pre commit versions (#3417)

Optimization​

  • Make Parquet merging much, much faster (60% faster) (#3403)

New Contributors​

Full Changelog: https://github.com/MultiQC/MultiQC/compare/v1.32...v1.33

MultiQC v1.32

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.

MultiQC v1.31

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.

MultiQC v1.27.1

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