ewels/MultiQC: MultiQC Version 1.3

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.

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 /).

• 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!
  • Module written by @rdali
• 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

• 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
  • Many of these spotted and fixed by @juliangehring
• Went through all modules and standardised plot titles
  • All plots should now have a title with the format Module name: Plot name

• New MultiQC docker image
  • Ready to use docker image now available at https://hub.docker.com/r/ewels/multiqc/ (200 MB)
  • Uses automated builds - pull :latest to get the development version, future releases will have stable tags.
  • Written by @MaxUlysse
• 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

• 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