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MultiQC Version 1.2
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@ewels ewels released this 16 Aug 10:33
v1.2
37510b4

CodeFest 2017 Contributions

We had a fantastic group effort on MultiQC at the 2017 BOSC CodeFest.
Many thanks to those involved!

New Modules:

  • AfterQC - New module!
    • Added parsing of the AfterQC json file data, with a plot of filtered reads.
    • Work by @raonyguimaraes
  • bcl2fastq
    • bcl2fastq can be used to both demultiplex data and convert BCL files to FASTQ file formats for downstream analysis
    • New module parses JSON output from recent versions and summarises some key statistics from the demultiplexing process.
    • Work by @iimog (with a little help from @tbooth and @ewels)
  • leeHom
    • leeHom is a program for the Bayesian reconstruction of ancient DNA
  • VCFTools
    • Added initial support for VCFTools relatedness2
    • Added support for VCFTools TsTv-by-count TsTv-by-qual TsTv-summary
    • Module written by @mwhamgenomics

Module updates:

  • FastQ Screen
    • Gracefully handle missing data from very old FastQ Screen versions.
  • RNA-SeQC
    • Add new transcript-associated reads plot.
  • Picard
    • New submodule to handle output from TargetedPcrMetrics
  • Prokka
    • Added parsing of the # CRISPR arrays data from Prokka when available (@asetGem)
  • Qualimap
    • Some code refactoring to radically improve performance and run times, especially with high coverage datasets.
    • Fixed bug where Cumulative coverage genome fraction plot could be truncated.

New MultiQC Features:

  • New module help text
    • Lots of additional help text was written to make MultiQC report plots easier to interpret.
    • Updated modules:
      • Bowtie
      • Bowtie 2
      • Prokka
      • Qualimap
      • SnpEff
    • Elite team of help-writers:
  • New config option section_comments allows you to add custom comments above specific sections in the report
  • New --tags and --view_tags command line options
    • Modules can now be given tags (keywords) and filtered by those. So running --tags RNA will only run MultiQC modules related to RNA analysis.
    • Work by @Hammarn
  • Back-end configuration options to specify the order of table columns
    • Modules and user configs can set priorities for columns to customise where they are displayed
    • Work by @tbooth
  • Added framework for proper unit testing
    • Previous start on unit tests tidied up, new blank template and tests for the clean_sample_name functionality.
    • Added to Travis and Appveyor for continuous integration testing.
    • Work by @tbooth
  • Bug fixes and refactoring of report configuration saving / loading
    • Discovered and fixed a bug where a report config could only be loaded once
    • Work by @DennisSchwartz
  • Table column row headers (sample names) can now be numeric-only.
  • Improved sample name cleaning functionality
    • Added option regex_keep to clean filenames by keeping the matching part of a pattern
    • Work by @robinandeer
  • Handle error when invalid regexes are given in reports
    • Now have a nice toast error warning you and the invalid regexes are highlighted
    • Previously this just crashed the whole report without any warning
    • Work by @robinandeer
  • Command line option --dirs-depth now sets -d to True (so now works even if -d isn't also specified).
  • New config option config.data_dump_file to export as much data as possible to multiqc_data/multiqc_data.json
  • New code to send exported JSON data to a a web server
    • This is in preparation for the upcoming MegaQC project. Stay tuned!

Bug Fixes:

  • Specifying multiple config files with -c/--config now works as expected
    • Previously this would only read the last specified
  • Fixed table rendering bug that affected Chrome v60 and IE7-11
    • Table cell background bars weren't showing up. Updated CSS to get around this rendering error.
  • HTML ID cleanup now properly cleans strings so that they work with jQuery as expected.
  • Made bar graph sample highlighting work properly again
  • Config custom_logo paths can now be relative to the config file (or absolute as before)
  • Report doesn't keep annoyingly telling you that toolbox changes haven't been applied
    • Now uses more subtle toasts and only when you close the toolbox (not every click).
  • Switching report toolbox options to regex mode now enables the Apply button as it should.
  • Sorting table columns with certain suffixes (eg. 13X) no works properly (numerically)
  • Fixed minor bug in line plot data smoothing (now works with unsorted keys)
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