MultiQC Version 0.9

@ewels ewels released this Dec 21, 2016 · 46 commits to master since this release

A major new feature is released in v0.9 - support for custom content. This means that MultiQC can now easily include output from custom scripts within reports without the need for a new module or plugin. For more information, please see the MultiQC documentation.

Module updates:

  • HTSeq - new module!
    • New module for the htseq-count tool, often used in RNA-seq analysis.
  • Prokka - new module!
    • Prokka is a software tool for the rapid annotation of prokaryotic genomes.
  • Slamdunk - new module!
    • Slamdunk is a software tool to analyze SLAMSeq data.
  • Peddy - new module!
    • Peddy calculates genotype :: pedigree correspondence checks, ancestry checks and sex checks using VCF files.
  • Cutadapt
    • Fixed bug in General Stats table number for old versions of cutadapt (pre v1.7)
    • Added support for really old cutadapt logs (eg. v.1.2)
  • FastQC
    • New plot showing total overrepresented sequence percentages.
    • New option to parse a file containing a theoretical GC curve to display in the background.
  • featureCounts
    • Added parsing checks and catch failures for when non-featureCounts files are picked up by accident
  • GATK
    • Fixed logger error in VariantEval module.
  • Picard
    • Fixed missing sample overwriting bug in RnaSeqMetrics
    • New feature to customise coverage shown from HsMetrics in General Statistics table
      see the docs for info).
    • Fixed compatibility problem with output from CollectMultipleMetrics for CollectAlignmentSummaryMetrics
  • Preseq
    • Module now recognises output from c_curve mode.
  • RSeQC
    • Made the gene body coverage plot show the percentage view by default
    • Made gene body coverage properly handle sample names
  • Samtools
    • New module to show duplicate stats from rmdup logs
    • Fixed a couple of niggles in the idxstats plot
  • SnpEff
    • Fixed swapped axis labels in the Variant Quality plot
  • STAR
    • Fixed crash when there are 0 unmapped reads.
    • Sample name now taken from the directory name if no file prefix found.
  • Qualimap BamQC
    • Add a line for pre-calculated reference genome GC content
    • Plot cumulative coverage for values above 50x, align with the coverage histogram.
    • New ability to customise coverage thresholds shown in General Statistics table
      (see the docs for info).

Core Updates:

  • Support for custom content (see top of release notes).
  • New ninja report tool: make scatter plots of any two table columns!
  • Plot data now saved in multiqc_data when 'flat' image plots are created
    • Allows you easily re-plot the data (eg. in Excel) for further downstream investigation
  • Added 'Apply' button to Highlight / Rename / Hide.
    • These tools can become slow with large reports. This means that you can enter several
      things without having to wait for the report to replot each change.
  • Report heatmaps can now be sorted by highlight
  • New config options decimalPoint_format and thousandsSep_format
    • Allows you to change the default 1 234.56 number formatting for plots.
  • New config option top_modules allows you to specify modules that should come at the top of the report
  • Fixed bar plot bug where missing categories could shift data between samples
  • Report title now printed in the side navigation
  • Missing plot IDs added for easier plot exporting
  • Stopped giving warnings about skipping directories (now a debug message)
  • Added warnings in report about missing functionality for flat plots (exporting and toolbox)
  • Export button has contextual text for images / data
  • Fixed a bug where user config files were loaded twice
  • Fixed bug where module order was random if --module or --exclude was used.
  • Refactored code so that the order of modules can be changed in the user config
  • Beefed up code + docs in scatter plots back end and multiple bar plots.
  • Fixed a few back end nasties for Tables
    • Shared-key columns are no longer forced to share colour schemes
    • Fixed bug in lambda modified values when format string breaks
    • Supplying just data with no header information now works as advertised
  • Improvements to back end code for bar plots
    • New tt_decimals and tt_suffix options for bar plots
    • Bar plots now support yCeiling, yFloor and yMinRange, as with line plots.
    • New option hide_zero_cats:False to force legends to be shown even when all data is 0
  • General Stats Showing x of y columns count is fixed on page load.
  • Big code whitespace cleanup

Downloads

MultiQC Version 0.8

@ewels ewels released this Sep 26, 2016 · 215 commits to master since this release

Module updates:

  • GATK - new module!
    • Added support for VariantEval reports, only parsing a little of the information
      in there so far, but it's a start.
    • Module originally written by @robinandeer at the OBF Codefest,
      finished off by @ewels
  • 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.
  • Bowtie1
    • Updated to try to find bowtie command before log, handle multiple logs in one file. Same as bowtie2.
  • FastQC
    • Sample pass/warn/fail lists now display properly even with large numbers of samples
    • Sequence content heatmap display is better with many samples
  • Kallisto
    • Now supports logs from SE data.
  • Picard
    • BaseDistributionByCycle - new submodule! Written by @mlusignan
    • RnaSeqMetrics - new submodule! This one by @ewels ;)
    • AlignmentSummaryMetrics - another new submodule!
    • Fixed truncated files crash bug for Python 3 (#306)
  • Qualimap RNASeqQC
    • Fixed parsing bug affecting counts in Genomic Origin plot.
    • Module now works with European style thousand separators (1.234,56 instead of 1,234.56)
  • RSeQC
    • infer_experiment - new submodule! Written by @Hammarn
  • Samtools
    • stats submodule now has separate bar graph showing alignment scores
    • flagstat - new submodule! Written by @HLWiencko
    • idxstats - new submodule! This one by @ewels again

Core updates:

  • New --export/-p option to generate static images plot in multiqc_plots (.png, .svg and .pdf)
    • Configurable with export_plots, plots_dir_name and export_plot_formats config options
    • --flat option no longer saves plots in multiqc_data/multiqc_plots
  • New --comment/-b flag to add a comment to the top of reports.
  • New --dirs-depth/-dd flag to specify how many directories to prepend with --dirs/-d
    • Specifying a postive number will take that many directories from the end of the path
    • A negative number will take directories from the start of the path.
  • Directory paths now appended before cleaning, so fn_clean_exts will now affect these names.
  • New custom_logo attributes to add your own logo to reports.
  • New report_header_info config option to add arbitrary information to the top of reports.
  • New --pdf option to create a PDF report
    • Depends on Pandoc being installed and is in a beta-stage currently.
    • Note that specifying this will make MultiQC use the simple template, giving a HTML report with
      much reduced functionality.
  • New fn_clean_sample_names config option to turn off sample name cleaning
    • This will print the full filename for samples. Less pretty reports and rows
      on the General Statistics table won't line up, but can prevent overwriting.
  • Table header defaults can now be set easily
  • General Statistics table now hidden if empty.
  • Some new defaults in the sample name cleaning
  • Updated the simple template.
    • Now has no toolbox or nav, no JavaScript and is better suited for printing / PDFs.
    • New config.simple_output config flag so code knows when we're trying to avoid JS.
  • 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.
  • Fixed nasty bug in beeswarm dot plots where sample names were mixed up (#278)
  • Beeswarm header text is now more informative (sample count with more info on a tooltip)
  • Beeswarm plots now work when reports have > 1000 samples

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

Downloads

MultiQC Version 0.7

@ewels ewels released this Jul 4, 2016 · 350 commits to master since this release

Version 0.7 of MultiQC!

This is quite a big release: 141 commits since v0.6, with 4,587 new lines of code and 2,116 lines deleted (or updated), affecting 75 files. Many thanks to everyone for your patience.

MultiQC is published!

If you didn't hear about it - the reason that I wanted to keep the main release stable was because the MultiQC paper was under review. It went well, and MultiQC is now published! You can see it here:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

Many thanks to everyone involved.

Module updates:

Not a huge number of new modules this time, but lots of fixed bugs and quite a few big extensions / refactoring of big modules.

  • 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 Galaxy! 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.

Downloads

MultiQC Version 0.6

@ewels ewels released this Apr 29, 2016 · 491 commits to master since this release

Date released: 2016-04-29

Key highlights in this report are new plot types! Beeswarm and generalised tables. Three new modules, a major internal code refactoring around plotting and tables (now easier to understand, maintain and add to) and a whole swath of other minor module updates, new functions and features..

Changelog:

  • 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

Downloads

MultiQC v0.5

@ewels ewels released this Mar 29, 2016 · 594 commits to master since this release

Latest version of MultiQC. Key highlights are big reports (hundreds / thousands of samples now possible), numerous new modules, better plugin framework and a bunch of tweaks for smoother running.

Changelog:

  • 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

Downloads

MultiQC v0.4

@ewels ewels released this Feb 16, 2016 · 696 commits to master since this release

Latest release of MultiQC with some tasty new functions..

  • 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

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MultiQC v0.3.2

@ewels ewels released this Feb 8, 2016 · 721 commits to master since this release

New version - a number of new modules, a few new command line options and some new toys in the report user interface.

I've just noticed that this was a bugfix version number bump and it should have been a minor version bump (v0.4). But I've already pushed this to PyPI so I'm not going to change it now. Sorry.

Anyway, here's what's new:

Changelog

  • 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

Downloads

MultiQC v0.3.1

@ewels ewels released this Nov 4, 2015 · 828 commits to master since this release

Hotfix to patch a bug that I found immediately after submitting v0.3.0 - sorry! Took the opportunity to add a few more new things to sweeten the deal.

Changelog

  • 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.

Downloads

MultiQC v0.3

@ewels ewels released this Nov 4, 2015 · 833 commits to master since this release

Lots of spit and polish added to MultiQC in this release - everything should now be properly documented and reports are quite a bit more stable.

Changelog

  • 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.

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MultiQC v0.2

@ewels ewels released this Sep 18, 2015 · 1047 commits to master since this release

A major rewrite of MultiQC, with a lot of stabilisation and sanitisation. Many new functions created in Python and JavaScript to handle common functions, making writing new modules much easier. New toolbox of features created for report, making it much more interactive.

Download MultiQC_v0.2.app.zip for the Mac OS X graphical tool. To run from the command line, download the zip of the code. Can also be installed directly with pip from PyPI:

pip install multiqc

Downloads