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CHANGELOG.md

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MultiQC Version History

v0.8dev

Module updates:

  • Bcftools - new module!
  • QUAST - new module!
    • QUAST is a tool for assessing de novo assemblies against reference genomes.
  • Bismark now supports reports from bam2nuc, giving Cytosine coverage in General Stats.
  • Samtools
    • stats submodule now has separate bar graph showing alignment scores
    • flagstat - new submodule! Written by @HLWiencko
  • Picard
    • BaseDistributionByCycle - new submodule! Written by @mlusignan

Core updates:

  • New custom_logo attributes to add your own logo to reports.
  • New --proj-info flag to add arbitrary information to the top of reports.
  • Table header defaults can now be set easily
  • General Statistics table now hidden if empty.
  • Fixed some bugs with config settings (eg. template) being overwritten.
  • NFS log file deletion bug fixed by @brainstorm (#265)
  • Fixed bug in --ignore behaviour with directory names.

Many thanks to those at the OpenBio Codefest 2016 who worked on MultiQC projects.

v0.7 - 2016-07-04

Module updates:

  • Kallisto - new module!
  • Picard
    • Code refactored to make maintenance and additions easier.
    • Big update to HsMetrics parsing - more results shown in report, new plots (by @lpantano)
    • Updated InsertSizeMetrics to understand logs generated by CollectMultipleMetrics (#215)
    • Newlines in picard output. Fixed by @dakl
  • Samtools
    • Code refactored
    • Rewrote the samtools stats code to display more stats in report with a beeswarm plot.
  • Qualimap
    • Rewritten to use latest methods and fix bugs.
    • Added Percentage Aligned column to general stats for BamQC module.
    • Extra table thresholds added by @avilella (hidden by default)
  • General Statistics
    • Some tweaks to the display defaults (FastQC, Bismark, Qualimap, SnpEff)
    • Now possible to skip the General Statistics section of the report with --exclude general_stats
  • Cutadapt module updated to recognise logs from old versions of cutadapt (<= v1.6)
  • Trimmomatic
    • Now handles , decimal places in percentage values.
    • Can cope with line breaks in log files (see issue #212)
  • FastQC refactored
    • Now skips zip files if the sample name has already been found. Speeds up MultiQC execution.
    • Code cleaned up. Parsing and data-structures standardised.
    • New popovers on Pass / Warn / Fail status bars showing sample names. Fast highlighting and hiding.
    • New column in General Stats (hidden by default) showing percentage of FastQC modules that failed.
  • SnpEff
    • Search pattern now more generic, should match reports from others.
    • Counts by Effect plot removed (had hundreds of categories, was fairly unusable).
    • KeyError bug fixed.
  • Samblaster now gets sample name from ID instead of SM (@dakl)
  • Bowtie 2
    • Now parses overall alignment rate as intended.
    • Now depends on even less log contents to work with more inputs.
  • MethylQA now handles variable spacing in logs
  • featureCounts now splits columns on tabs instead of whitespace, can handle filenames with spaces

Core updates:

  • Galaxy: MultiQC now available in Galax! Work by @devengineson / @yvanlebras / @cmonjeau
  • Heatmap: New plot type!
  • Scatter Plot: New plot type!
  • Download raw data behind plots in reports! Available in the Export toolbox.
    • Choose from tab-separated, comma-separated and the complete JSON.
  • Table columns can be hidden on page load (shown through Configure Columns)
    • Defaults are configurable using the table_columns_visible config option.
  • Beeswarm plot: Added missing rename / highlight / hiding functionality.
  • New -l / --file-list option: specify a file containing a list of files to search.
  • Updated HighCharts to v4.2.5. Added option to export to JPEG.
  • Can now cancel execution with a single ctrl+c rather than having to button mash
  • More granular control of skipping files during scan (filename, dirname, path matching)
    • Fixed --exclude so that it works with directories as well as files
  • New Clear button in toolbox to bulk remove highlighting / renaming / hiding filters.
  • Improved documentation about behaviour for large sample numbers.
  • Handle YAML parsing errors for the config file more gracefully
  • Removed empty columns from tables again
  • Fixed bug in changing module search patterns, reported by @lweasel
  • Added timeout parameter to version check to prevent hang on systems with long defaults
  • Fixed table display bug in Firefox
  • Fixed bug related to order in which config files are loaded
  • Fixed bug that broke the "Show only" toolbox feature with multiple names.
  • Numerous other small bugs.

v0.6 - 2016-04-29

Module updates:

  • 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
  • Added percentage view to Picard insert size plot

Core updates:

  • 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.

Bugfixes:

  • Qualimap handles infinity symbol (thanks @chapmanb )
  • Made SnpEff less fussy about required fields for making plots
  • UTF-8 file paths handled properly in Py2.7+
  • Extending two config variables wasn't working. Now fixed.
  • Dragging the height bar of plots now works again.
  • Plots now properly change y axis limits and labels when changing datasets
  • Flat plots now have correct path in default_dev template

v0.5 - 2016-03-29

Module updates:

Core updates:

  • 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.