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MultiQC Version 1.4
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@ewels ewels released this 11 Jan 14:25
v1.4
baefc2e

A slightly earlier-than-expected release due to a new problem with dependency packages that is breaking MultiQC installations since 2018-01-11.

New Modules:

  • Sargasso
    • Parses output from Sargasso - a tool to separate mixed-species RNA-seq reads according to their species of origin
    • Module written by @hxin
  • VerifyBAMID
    • Parses output from VerifyBAMID - a tool to detect contamination in BAM files.
    • Adds the CHIPMIX and FREEMIX columns to the general statistics table.
    • Module written by @aledj2

Module updates:

  • MACS2
    • Updated to work with output from older versions of MACS2 by @avilella
  • Peddy
    • Add het check plot to suggest potential contamination by @aledj2
  • Picard
    • Picard HsMetrics HS_PENALTY plot now has correct axis labels
    • InsertSizeMetrics switches commas for points if it can't convert floats. Should help some european users.
  • QoRTs
    • Added support for new style of output generated in the v1.3.0 release
  • Qualimap
    • New Error rate column in General Statistics table, added by @Cashalow
      • Hidden by default - customise your MultiQC config to always show this column (see docs)
  • QUAST
    • New option to customise the default display of contig count and length (eg. bp instead of Mbp).
    • See documentation. Written by @ewels and @Cashalow
  • RSeQC
    • Removed normalisation in Junction Saturation plot. Now raw counts instead of % of total junctions.

New MultiQC Features:

  • Conditional formatting / highlighting of cell contents in tables
    • If you want to make values that match a criteria stand out more, you can now write custom rules and formatting instructions for tables.
    • For instructions, see the documentation
  • New --lint option which is strict about best-practices for writing new modules
    • Useful when writing new modules and code as it throws warnings
    • Currently only implemented for bar plots and a few other places. More linting coming soon...
  • If MultiQC breaks and shows am error message, it now reports the filename of the last log it found
    • Hopefully this will help with debugging / finding dodgy input data

Bug Fixes

  • Addressed new dependency error with conflicting package requirements
    • There was a conflict between the networkx, colormath and spectra releases.
    • I previously forced certain software versions to get around this, but spectra has now updated with the unfortunate effect of introducing a new dependency clash that halts installation.
  • Fixed newly introduced bug where Custom Content MultiQC config file search patterns had been broken
  • Updated pandoc command used in --pdf to work with new releases of Pandoc
  • Made config table_columns_visible module name key matching case insensitive to make less frustrating
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