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MultiQC Version 1.3
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@ewels ewels released this 03 Nov 13:36
v1.3
1514bff

There are 34 merged pull-requests in this release - a fantastic example of how an open source community can develop a tool! Many thanks to everyone involved for their hard work.

Breaking changes - custom search patterns

Only for users with custom search patterns for the bowtie or star: you will
need to update your config files - the bowtie search key is now bowtie1,
star_genecounts is now star/genecounts.

For users with custom modules - search patterns must now conform to the search
pattern naming convention: modulename or modulename/anything (the search pattern
string beginning with the name of your module, anything you like after the first /).

New Modules:

  • 10X Supernova
    • Parses statistics from the de-novo Supernova software.
    • Module written by @remiolsen
  • BBMap
    • Plot metrics from a number of BBMap tools, a suite of DNA/RNA mapping tools and utilities
    • Module written by @boulund and @epruesse
  • deepTools - new module!
    • Parse text output from bamPEFragmentSize, estimateReadFiltering, plotCoverage, plotEnrichment, and plotFingerprint
    • Module written by @dpryan79
  • Homer Tag Directory - new submodule!
  • illumina InterOp
    • Module to parse metrics from illumina sequencing runs and demultiplexing, generated by the InterOp package
    • Module written by @matthdsm
  • RSEM - new module!
    • Parse .cnt file comming from rsem-calculate-expression and plot read repartitions (Unalignable, Unique, Multi ...)
    • Module written by @noirot
  • HiCExplorer
    • New module to parse the log files of hicBuildMatrix.
    • Module written by @joachimwolff

Module updates:

  • AfterQC
    • Handle new output format where JSON summary key changed names.
  • bcl2fastq
    • Clusters per sample plot now has tab where counts are categoried by lane.
  • GATK
    • New submodule to handle Base Recalibrator stats, written by @winni2k
  • HiSAT2
    • Fixed bug where plot title was incorrect if both SE and PE bargraphs were in one report
  • Picard HsMetrics
    • Parsing code can now handle commas for decimal places
  • Preseq
    • Updated odd file-search pattern that limited input files to 500kb
  • QoRTs
    • Added new plots, new helptext and updated the module to produce a lot more output.
  • Qualimap BamQC
    • Fixed edge-case bug where the refactored coverage plot code could raise an error from the range call.
  • Documentation and link fixes for Slamdunk, GATK, bcl2fastq, Adapter Removal, FastQC and main docs
  • Went through all modules and standardised plot titles
    • All plots should now have a title with the format Module name: Plot name

New MultiQC Features:

  • New MultiQC docker image
  • New module_order config options allow modules to be run multiple times
    • Filters mean that a module can be run twice with different sets of files (eg. before and after trimming)
    • Custom module config parameters can be passed to module for each run
  • File search refactored to only search for running modules
    • Makes search much faster when running with lots of files and limited modules
    • For example, if using -m star to only use the STAR module, all other file searches now skipped
  • File search now warns if an unrecognised search type is given
  • MultiQC now saves nearly all parsed data to a structured output file by default
    • See multiqc_data/multiqc_data.json
    • This can be turned off by setting config.data_dump_file: false
  • Verbose logging when no log files found standardised. Less duplication in code and logs easier to read!
  • New documentation section describing how to use MultiQC with Galaxy
  • Using shared_key: 'read_counts' in table header configs now applies relevant defaults

Bug Fixes

  • Installation problem caused by changes in upstream dependencies solved by stricter installation requirements
  • Minor default_dev directory creation bug squashed
  • Don't prepend the directory separator (|) to sample names with -d when there are no subdirs
  • yPlotLines now works even if you don't set width
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