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MultiQC Version 0.9
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@ewels ewels released this 21 Dec 16:14
v0.9
56112ea

A major new feature is released in v0.9 - support for custom content. This means that MultiQC can now easily include output from custom scripts within reports without the need for a new module or plugin. For more information, please see the MultiQC documentation.

Module updates:

  • HTSeq - new module!
    • New module for the htseq-count tool, often used in RNA-seq analysis.
  • Prokka - new module!
    • Prokka is a software tool for the rapid annotation of prokaryotic genomes.
  • Slamdunk - new module!
    • Slamdunk is a software tool to analyze SLAMSeq data.
  • Peddy - new module!
    • Peddy calculates genotype :: pedigree correspondence checks, ancestry checks and sex checks using VCF files.
  • Cutadapt
    • Fixed bug in General Stats table number for old versions of cutadapt (pre v1.7)
    • Added support for really old cutadapt logs (eg. v.1.2)
  • FastQC
    • New plot showing total overrepresented sequence percentages.
    • New option to parse a file containing a theoretical GC curve to display in the background.
  • featureCounts
    • Added parsing checks and catch failures for when non-featureCounts files are picked up by accident
  • GATK
    • Fixed logger error in VariantEval module.
  • Picard
    • Fixed missing sample overwriting bug in RnaSeqMetrics
    • New feature to customise coverage shown from HsMetrics in General Statistics table
      see the docs for info).
    • Fixed compatibility problem with output from CollectMultipleMetrics for CollectAlignmentSummaryMetrics
  • Preseq
    • Module now recognises output from c_curve mode.
  • RSeQC
    • Made the gene body coverage plot show the percentage view by default
    • Made gene body coverage properly handle sample names
  • Samtools
    • New module to show duplicate stats from rmdup logs
    • Fixed a couple of niggles in the idxstats plot
  • SnpEff
    • Fixed swapped axis labels in the Variant Quality plot
  • STAR
    • Fixed crash when there are 0 unmapped reads.
    • Sample name now taken from the directory name if no file prefix found.
  • Qualimap BamQC
    • Add a line for pre-calculated reference genome GC content
    • Plot cumulative coverage for values above 50x, align with the coverage histogram.
    • New ability to customise coverage thresholds shown in General Statistics table
      (see the docs for info).

Core Updates:

  • Support for custom content (see top of release notes).
  • New ninja report tool: make scatter plots of any two table columns!
  • Plot data now saved in multiqc_data when 'flat' image plots are created
    • Allows you easily re-plot the data (eg. in Excel) for further downstream investigation
  • Added 'Apply' button to Highlight / Rename / Hide.
    • These tools can become slow with large reports. This means that you can enter several
      things without having to wait for the report to replot each change.
  • Report heatmaps can now be sorted by highlight
  • New config options decimalPoint_format and thousandsSep_format
    • Allows you to change the default 1 234.56 number formatting for plots.
  • New config option top_modules allows you to specify modules that should come at the top of the report
  • Fixed bar plot bug where missing categories could shift data between samples
  • Report title now printed in the side navigation
  • Missing plot IDs added for easier plot exporting
  • Stopped giving warnings about skipping directories (now a debug message)
  • Added warnings in report about missing functionality for flat plots (exporting and toolbox)
  • Export button has contextual text for images / data
  • Fixed a bug where user config files were loaded twice
  • Fixed bug where module order was random if --module or --exclude was used.
  • Refactored code so that the order of modules can be changed in the user config
  • Beefed up code + docs in scatter plots back end and multiple bar plots.
  • Fixed a few back end nasties for Tables
    • Shared-key columns are no longer forced to share colour schemes
    • Fixed bug in lambda modified values when format string breaks
    • Supplying just data with no header information now works as advertised
  • Improvements to back end code for bar plots
    • New tt_decimals and tt_suffix options for bar plots
    • Bar plots now support yCeiling, yFloor and yMinRange, as with line plots.
    • New option hide_zero_cats:False to force legends to be shown even when all data is 0
  • General Stats Showing x of y columns count is fixed on page load.
  • Big code whitespace cleanup
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