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@vladsavelyev vladsavelyev released this 09 Jul 10:23
v1.30
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MultiQC v1.30 - 2025-07-09

Minor improvements and fixes.

Feature updates

  • Support markdown in custom content (#3204)
  • Support reasoning models in AI summaries (#3265)
  • Always save AI prompt to file as llms-full.txt (#3257)
  • Allow Plotly theme configuration with config.plot_theme (#3250)
  • Use polars-lts-cpu library for polars for better CPU compatibility across Docker containers (#3240)
  • Allow adding any metric from multiqc_data.json to general stats with config.general_stats_columns (#3245)
  • Box plot: dynamically determine whether to show interactive points for outliers (similar to violin plots). Add boxplot_boxpoints config option to override it explicitly (#3244, #3248)
  • Detect AI provider for summaries from environment variables (#3254)
  • Scatter plot: allow custom marker symbol (#3234)
  • Use universal config.use_filename_as_sample_name config flag for modules, and deprecate module-specific flags (3241)
  • Allow multi-line info sections in module sections (#3225)
  • AI summaries: update the model defaults (default to Claude 4) (#3265)
  • Color schemes: lighten colours with alpha instead of admixing white (#3252)
  • Performance: use OrderedDict for saved_raw_data_keys (#3235)

Fixes

  • Custom content line plots: allow passing data as a list of tuples in JSON to avoid ordering issues (#3246)
  • Fix merging modules from multiple parquet files (#3267)
  • Fix series labels in heatmap subtitle (#3260)
  • Fix custom content description when grouping section with parent_id (#3242)
  • Fix timezone issue in parquet export (#3224)

Module updates and fixes

  • Elembio bases2fastq: fix PE bug, add % bases below PF plot (#3233)
  • Picard: support sentieon for WgsMetrics (#3200)
  • Picard: new OxoGMetrics search pattern (#3212)
  • VEP: support version 114 (#3209)
  • samtools: support ampliconclip stats (#3214)
  • Percolator: handle comments in parsing (#3217)
  • RSeQC: normalise junction saturation plot (#3216)
  • Somalier: fix sex plot description (#3261)
  • FastQC: fix subtitle in status check heatmap and adapters content plot (#3260)
  • Cutadapt: fix extracting sample name from command line params (#3262)
  • UMItools: bump up search pattern checked number of lines (#3263)
  • Samtools: allow configuring metrics to add to general stats with config.general_stats_columns (#3245)
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