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MultiQC v1.25.2

MultiQC

Multiple bug fixes and minor updates.

Feature updates and improvements​

  • Add natural sort for sample sorting (#2959)
  • Custom content: for plot_type: image, support custom_data config with section name and description. Fix misleading logging (#2939)
  • Config validation improvements (group messages, cast types, validate column headers) (#2899)

Fixes​

  • Workaround for displaying sample grouping in Safari because of missing visibility: collapse (#2941)
  • Fix table CSV export where a title contains a comma (#2911)
  • Showing table in notebooks: respect col1_header (#2914)
  • Customizing custom_table_header_config: fix docs, support both the old and the new ways (#2955)
  • Table scatter mini-plots: fix rounding and range (#2956)
  • File line block iterator: fix reading long lines that do not fit one block (#2935)
  • Fix cond_formatting_rules type hint to avoid validation error (#2922)
  • Fix config.prepend_dirs or -d -dd 1 (#2913)
  • Sample grouping fixes (#2920):
    • Keep sample name column fix width to avoid jumping
    • Fix hiding columns through the modal
  • Custom content fixes:
    • Avoid showing section_comment both for module and section when they have the same ID (#2954)
    • Address issue of sections without search patterns and headers in files (#2921)
    • Fix duplicated custom content sections in the report (#2921)
    • Fix support for plot_type: violin (#2957)

Module updates​

  • ngsbits: add submodule samplegender (#2854)
  • nanoq: change lineplots for barplots (#2934)
  • Qualimap: clarify the direction of the transcript in coverage plot (#2946)
  • picard: add table with all metrics to VariantCallingMetrics section (#2885)
  • Nanostat: add general stats columns (#2961)
  • Samtools: add insert size to general stats table (#2905)

Module fixes​

  • bcl2fastq: fix missing R1_*/R2_* metrics (#2965)
  • Cutadapt: fix for null values from r2 data (#2936)
  • Qualimap: fix parsing ∞ value (#2937)
  • bclconvert: fix undetermined barcodes plot (#2976)
  • featurecounts: fix missing section name and anchor (#2967)

Infrastructure​

  • Pin kaleido to 0.2.1 (new 0.4.1 does not embed a browser and thus not portable) (#2963)