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MultiQC Version 1.5
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@ewels ewels released this 15 Mar 15:55
v1.5
32c35ee

New Modules:

  • DeDup - New module!
    • DeDup: Improved Duplicate Removal for merged/collapsed reads in ancient DNA analysis
    • Module written by @apeltzer,
  • Clip&Merge - New module!
    • Clip&Merge: Adapter clipping and read merging for ancient DNA analysis
    • Module written by @apeltzer,

Module updates:

  • bcl2fastq
    • Catch ZeroDivisionError exceptions when there are 0 reads (@aledj2)
    • Add parsing of TrimmedBases and new General Stats column for % bases trimmed (@matthdsm).
  • BUSCO
    • Fixed configuration bug that made all sample names become 'short'
  • Custom Content
    • Parsed tables now exported to multiqc_data files
  • Cutadapt
    • Refactor parsing code to collect all length trimming plots
  • FastQC
    • Fixed starting y-axis label for GC-content lineplot being incorrect.
  • HiCExplorer
    • Updated to work with v2.0 release.
  • Homer
    • Made parsing of tagInfo.txt file more resilient to variations in file format so that it works with new versions of Homer.
    • Kept order of chromosomes in coverage plot consistent.
  • Peddy
    • Switch Sex error logic to Correct sex for better highlighting (@aledj2)
  • Picard
    • Updated module and search patterns to recognise new output format from Picard version >= 2.16 and GATK output.
  • Qualimap BamQC
    • Fixed bug where start of Genome Fraction could have a step if target is 100% covered.
  • RNA-SeQC
    • Added rRNA alignment stats to summary table @Rolandde
  • RSeqC
    • Fixed read distribution plot by adding category for other_intergenic (thanks to @moxgreen)
    • Fixed a dodgy plot title (Read GC content)
  • Supernova
    • Added support for Supernova 2.0 reports. Fixed a TypeError bug when using txt reports only. Also a bug when parsing empty histogram files.

New MultiQC Features:

  • Invalid choices for --module or --exclude now list the available modules alphabetically.
  • Linting now checks for presence in config.module_order and tags.

Bug Fixes

  • Excluding modules now works in combination with using module tags.
  • Fixed edge-case bug where certain combinations of output_fn_name and data_dir_name could trigger a crash
  • Conditional formatting - values are now longer double-labelled
  • Made config option extra_series work in scatter plots the same way that it works for line plots
  • Locked the matplotlib version to v2.1.0 and below
    • Due to two bugs that appeared in v2.2.0 - will remove this constraint when there's a new release that works again.
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