MultiQC: summarize analysis results for multiple tools and samples in a single report

MultiQC v1.25 - 2024-09-16

Highlights - sample grouping

New feature: grouping samples in the General Statistics table.

<img width="400" src="docs/images/changelog/v1.25-grouping-samples.png">

Some modules - prominently FastQC - may produce multiple results per sample, e.g. for the forward and the reverse reads. To group such results in the table together, a new configuration option is introduced.

This feature is currently opt-in, you'll need to set table_sample_merge in a MultiQC config file to use (see docs above). We'd love to hear your feedback! We hope to enable it by default for common file suffix patterns in a future release.

Because MultiQC needs to know how to merge each column (sum, average, etc), each module must implement it independently. Currently it's supported by the FastQC and Cutadapt modules. If you'd like support added to another module, please let us know in a GitHub issue. Details of how to add it into module code can be found in the moduel development documentation.

Highlights - box plots in custom content

The new box plot plot type, added in v1.21, are now available to use with custom content! See 2847 for configuration examples.

New modules

• Add UMICollapse module (#2814)

Updates

• Group read pairs in general stats (#2794, #2848)
• Support boxplot in custom content (#2847)
• Allow x_band, x_lines, x_minrange for any plot type (specifically, scatter plots) (#2851)
• When both contents and contents_re are specified in a search patterns, treat it as logical AND (#2828)
• Add UMICollapse module (#2814)

Module updates

• NanoStat: support multi-sample logs (#2852)
• Samtools coverage: support exclude_contigs and include_contigs (#2840)
• Ganon: support non-verbose output, fix missing removed with --min-count (#2838)
• fastp: support the --merged flag (#2834)
• UMICollapse: support the FastQ mode. (#2827)

Fixes

• Workaround for the hanging Kaleido duing plot export: run plot export in separate threads with a timeout and fallback on freezes, add try-catch for crashes (#2836, #2819)
• Fix copying multiqc.log into the multiqc_data output folder (#2829)
• Fix applying exclude_files in search patterns (#2804)
• Fix bar plot export from toolbox (#2845)
• Fix autoselection in plot export toolbox (#2844)
• Fix config.replace_samples for custom content genstats table (#2841)

Module fixes

• Picard: fix parsing Sentieon insert size metrics (#2823)
• Picard: fix a search pattern of CollectRnaSeqMetrics (#2811)
• Kraken: fix for empty top ranks. Also handle it in bargraph (#2822)
• Cellranger: fix data source tag (#2821)
• FastQC: fix the Per Base Sequence Content detail plot click when a module was run multiple times (#2856)
• FastQC: fix calculating average read length (#2817)

Refactoring and typing

• Separate anchors and IDs for sections: use IDs for Python configation, and anchors in HTML (#2797, #2833)
• Prefix table column IDs with namespace, but allow configuration to use both short and long anchors (#2818)
• More type hinting in plots (#2816, #2850)
• Use typing.NewType for all Python versions (#2820)
• Remove pyaml_env dependency and apply the fix for the SyntaxWarning (#2837)

Infrastructure and packaging

• Add py.typed to mark package as providing type information (#2846)