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MultiQC v0.3.2
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@ewels ewels released this 08 Feb 13:46
v0.3.2
5e41208

New version - a number of new modules, a few new command line options and some new toys in the report user interface.

I've just noticed that this was a bugfix version number bump and it should have been a minor version bump (v0.4). But I've already pushed this to PyPI so I'm not going to change it now. Sorry.

Anyway, here's what's new:

Changelog

  • All modules now load their log file search parameters from a config
    file, allowing you to overwrite them using your user config file
    • This is useful if your analysis pipeline renames program outputs
  • New Picard (sub)modules - Insert Size, GC Bias & HsMetrics
  • New Qualimap (sub)module - RNA-Seq QC
  • Made Picard MarkDups show percent by default instead of counts
  • Added M-Bias plot to Bismark
  • New option to stream report HTML to stdout
  • Files can now be specified as well as directories
  • New options to specify whether the parsed data directory should be created
    • command line flags: --data / --no-data
    • config option name: make_data_dir
  • Fixed bug with incorrect path to installation dir config YAML file
  • New toolbox drawer for bulk-exporting graph images
  • Report side navigation can now be hidden to maximise horizontal space
  • Mobile styling improved for narrow screen
  • More vibrant colours in the general stats table
  • General stats table numbers now left aligned
  • Settings now saved and loaded to named localstorage locations
    • Simplified interface - no longer global / single report saving
    • Removed static file config. Solves JS error, no-one was doing this
      since we have standalone reports anyway.
  • Added support for Python 3.5
  • Fixed bug with module specific CSS / JS includes in some templates
  • Made the 'ignore files' config use unix style file pattern matching
  • Fixed some bugs in the FastQ Screen module
  • Fixed some bugs in the FastQC module
  • Fixed occasional general stats table bug
  • Table sorting on sample names now works after renaming
  • Bismark module restructure
    • Each report type now handled independently (alignment / dedup / meth extraction)
    • M-Bias plot now shows R1 and R2
  • FastQC GC content plot now has option for counts or percentages
    • Allows comparison between samples with very different read counts
  • Bugfix for reports javascript
    • Caused by updated to remotely loaded HighCharts export script
    • Export script now bundled with multiqc, so does not depend on internet connection
    • Other JS errors fixed in this work
  • Bugfix for older FastQC reports - handle old style sequence dup data
  • Bugfix for varying Tophat alignment report formats
  • Bugfix for Qualimap RNA Seq reports with paired end data
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