CHANGELOG.md

MultiQC Version History

v0.7dev

• Refactored Picard and Samtools code to make maintenance and additions easier.
• Rewrote the samtools stats code to display more stats in report with a beeswarm plot.
• Added missing rename / highlight / hiding functionality to new beeswarm plot.
• Updated HighCharts to v4.2.5. Added option to export to JPEG.
• Bugfix: Removed empty columns from tables again
• Bugfix: Newlines in picard output. Fixed by @dakl

v0.6 - 2016-04-29

• New Salmon module.
• New Trimmomatic module.
• New Bamtools stats module.
• New beeswarm plot type. General Stats table replaced with this when many samples in report.
• New RSeQC module: Actually a suite of 8 new modules supporting various outputs from RSeQC
• Rewrote bowtie2 module: Now better at parsing logs and tries to scrape input from wrapper logs.
• Made cutadapt show counts by default instead of obs/exp
• Dynamic plots now update their labels properly when changing datasets and to percentages
• Config files now loaded from working directory if present
• Started new docs describing how each module works
• Refactored featureCounts module. Now handles summaries describing multiple samples.
• Stopped using so many hidden files. .multiqc.log now called multiqc.log
• New -c/--config command line option to specify a MultiQC configuration file
• Can now load run-specific config files called multiqc_config.yaml in working directory
• Large code refactoring - moved plotting code out of BaseModule and into new multiqc.plots submodules
• Generalised code used to generate the General Stats table so that it can be used by modules
• Removed interactive report tour, replaced with a link to a youtube tutorial
• Made it possible to permanently hide the blue welcome message for all future reports
• New option to smooth data for line plots. Avoids mega-huge plots. Applied to SnpEff, RSeQC, Picard.
• Added percentage view to Picard insert size plot
• Bugfix: Qualimap handles infinity symbol (thanks @chapmanb )
• Bugfix: Made SnpEff less fussy about required fields for making plots
• Bufgix: UTF-8 file paths handled properly in Py2.7+
• Bugfix: Extending two config variables wasn't working. Now fixed.
• Bugfix: Dragging the height bar of plots now works again.
• Bugfix: Plots now properly change y axis limits and labels when changing datasets
• Bugfix: Flat plots now have correct path in default_dev template

v0.5 - 2016-03-29

• New Skewer module, written by @dakl
• New Samblaster module, written by @dakl
• New Samtools stats module, written by @lpantano
• New HiCUP module
• New SnpEff module
• New methylQA module
• New "Flat" image plots, rendered at run time with MatPlotLib
  • By default, will use image plots if > 50 samples (set in config as plots_flat_numseries)
  • Means that very large numbers of samples can be viewed in reports. eg. single cell data.
  • Templates can now specify their own plotting functions
  • Use --flat and --interactive to override this behaviour
• MultiQC added to bioconda (with help from @dakl)
• New plugin hook: config_loaded
• Plugins can now add new command line options (thanks to @robinandeer)
• Changed default data directory name from multiqc_report_data to multiqc_data
• Removed support for depreciated MultiQC_OSXApp
• Updated logging so that a verbose multiqc_data/.multiqc.log file is always written
• Now logs more stuff in verbose mode - command used, user configs and so on.
• Added a call to multiqc.info to check for new versions. Disable with config no_version_check
• Removed general stats manual row sorting.
• Made filename matching use glob unix style filename match patterns
• Everything (including the data directory) is now created in a temporary directory and moved when MultiQC is complete.
• A handful of performance updates for large analysis directories

v0.4 - 2016-02-16

• New multiqc_sources.txt which identifies the paths used to collect all report data for each sample
• Export parsed data as tab-delimited text, JSON or YAML using the new -k/--data-format command line option
• Updated HighCharts from v4.2.2 to v4.2.3, fixes tooltip hover bug.
• Nicer export button. Now tied to the export toolbox, hopefully more intuitive.
• FastQC: Per base sequence content heatmap can now be clicked to show line graph for single sample
• FastQC: No longer show adapter contamination datasets with <= 0.1% contamination.
• Picard: Added support for CollectOxoGMetrics reports.
• Changed command line option --name to --filename
• --name also used for filename if --filename not specified.
• Hide samples toolbox now has switch to show only matching samples
• New regex help box with examples added to report
• New button to copy general stats table to the clipboard
• General Stats table 'floating' header now sorts properly when scrolling
• Bugfix: MultiQC default_dev template now copies module assets properly
• Bufgix: General Stats table floating header now resizes properly when page width changes

v0.3.2 - 2016-02-08

• 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

v0.3.1 - 2015-11-04

• Hotfix patch to fix broken FastQC module (wasn't finding .zip files properly)
• General Stats table colours now flat. Should improve browser speed.
• Empty rows now hidden if appear due to column removal in general stats
• FastQC Kmer plot removed until we have something better to show.

v0.3 - 2015-11-04

• Lots of lovely new documentation!
• Child templates - easily customise specific parts of the default report template
• Plugin hooks - allow other tools to execute custom code during MultiQC execution
• New Preseq module
• New design for general statistics table (snazzy new background bars)
• Further development of toolbox
  • New button to clear all filters
  • Warnings when samples are hidden, plus empty plots and table cols are hidden
  • Active toolbar tab buttons are highlighted
• Lots of refactoring by @moonso to please the Pythonic gods
  • Switched to click instead of argparse to handle command line arguments
  • Code generally conforms to best practices better now.
• Now able to supply multiple directories to search for reports
• Logging output improved (now controlled by -q and -v for quiet and verbose)
• More HTML output dealt with by the base module, less left to the modules
  • Module introduction text
  • General statistics table now much easier to add to (new helper functions)
• Images, CSS and Javascript now included in HTML, meaning that there is a single report file to make sharing easier
• More accessible scrolling in the report - styled scrollbars and 'to top' button.
• Modules and templates now use setuptools entry points, facilitating plugins by other packages. Allows niche extensions whilst keeping the core codebase clean.
• The general stats table now has a sticky header row when scrolling, thanks to some new javascript wizardry...
• General stats columns can have a shared key which allows common colour schemes and data ranges. For instance, all columns describing a read count will now share their scale across modules.
• General stats columns can be hidden and reordered with a new modal window.
• Plotting code refactored, reports with many samples (>50 by default) don't automatically render to avoid freezing the browser.
• Plots with highlighted and renamed samples now honour this when exporting to different file types.

v0.2 - 2015-09-18

• Code restructuring for nearly all modules. Common base module functions now handle many more functions (plots, config, file import)
  • See the contributing notes for instructions on how to use these new helpers to make your own module
• New report toolbox - sample highlighting, renaming, hiding
  • Config is autosaved by default, can also export to a file for sharing
  • Interactive tour to help users find their way around
• New Tophat, Bowtie 2 and QualiMap modules
  • Thanks to @guillermo-carrasco for the QualiMap module
• Bowtie module now works
• New command line parameter -d prefixes sample names with the directory that they were found in. Allows duplicate filenames without being overwritten.
• Introduction walkthrough helps show what can be done in the report
• Now compatible with both Python 2 and Python 3
• Software version number now printed on command line properly, and in reports.
• Bugfix: FastQC doesn't break when only one report found
• Bugfix: FastQC seq content heatmap highlighting
• Many, many small bugfixes

v0.1 - 2015-09-01

• The first public release of MultiQC, after a month of development. Basic structure in place and modules for FastQC, FastQ Screen, Cutadapt, Bismark, STAR, Bowtie, Subread featureCounts and Picard MarkDuplicates. Approaching stability, though still under fairly heavy development.