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 )
Box plot: dynically determine whether to show interactive points for outliers (similar to violin plots), and add boxplot_boxpoints config option to override it explicitly (#3244 , #3248 )
Minor improvements
Custom content line plots: allow passing data as a list of tuples in JSON to avoid ordering issues (#3246 )
Allow adding any metric from multiqc_data.json to general stats with config.general_stats_columns (#3245 )
Detect AI provider from environment variables (#3254 )
Scatter plot: allow custom marker symbol (#3234 )
Use universal config.use_filename_as_sample_name config flag for modules, and depreate module-specific flags (3241 )
Allow multi-line info section in module sections (#3225 )
AI summaries: update model defaults (#3265 )
Color schemes: lighten colors with alpha instead of admixing white (#3252 )
Performance: use OrderedDict for saved_raw_data_keys (#3235 )
Fixes
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 )
