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MultiQC Version 1.9
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@ewels ewels released this 30 May 09:48
v1.9
a2597e3

Another massive release - many thanks to all of the contributors! Keep those pull-requests and issues coming!

Dropped official support for Python 2

Python 2 had its official sunset date
on January 1st 2020, meaning that it will no longer be developed by the Python community.
Part of the python.org statement reads:

That means that we will not improve it anymore after that day,
even if someone finds a security problem in it.
You should upgrade to Python 3 as soon as you can.

Very many Python packages no longer support Python 2
and it whilst the MultiQC code is currently compatible with both Python 2 and Python 3,
it is increasingly difficult to maintain compatibility with the dependency packages it
uses, such as MatPlotLib, numpy and more.

As of MultiQC version 1.9, Python 2 is no longer officially supported.
Automatic CI tests will no longer run with Python 2 and Python 2 specific workarounds
are no longer guaranteed.

Whilst it may be possible to continue using MultiQC with Python 2 for a short time by
pinning dependencies, MultiQC compatibility for Python 2 will now slowly drift and start
to break. If you haven't already, you need to switch to Python 3 now.

New MultiQC Features

  • Now using GitHub Actions for all CI testing
    • Dropped Travis and AppVeyor, everything is now just on GitHub
    • Still testing on both Linux and Windows, with multiple versions of Python
    • CI tests should now run automatically for anyone who forks the MultiQC repository
  • Linting with --lint now checks line graphs as well as bar graphs
  • New gathered template with no tool name sections (#1119)
  • Added --sample-filters option to add show/hide buttons at the top of the report (#1125)
    • Buttons control the report toolbox Show/Hide tool, filtering your samples
    • Allows reports to be pre-configured based on a supplied list of sample names at report-generation time.
  • Line graphs can now have Log10 buttons (same functionality as bar graphs)
  • Importing and running multiqc in a script is now a little Better
    • multiqc.run now returns the report and config as well as the exit code. This means that you can explore the MultiQC run time a little in the Python environment.
    • Much more refactoring is needed to make MultiQC as useful in Python scripts as it could be. Watch this space.
  • If a custom module anchor is set using module_order, it's now used a bit more:
    • Prefixed to module section IDs
    • Appended to files saved in multiqc_data
    • Should help to prevent duplicates requiring -1 suffixes when running a module multiple times
  • New heatmap plot config options xcats_samples and ycats_samples
    • If set to False, the report toolbox options (highlight, rename, show/hide) do not affect that axis.
    • Means that the Show only matching samples report toolbox option works on FastQC Status Checks, for example (#1172)
  • Report header time and analysis paths can now be hidden
    • New config options show_analysis_paths and show_analysis_time (#1113)
  • New search pattern key skip: true to skip specific searches when modules look for a lot of different files (eg. Picard).
  • New --profile-runtime command line option (config.profile_runtime) to give analysis of how long the report takes to be generated
    • Plots of the file search results and durations are added to the end of the MultiQC report as a special module called Run Time
    • A summary of the time taken for the major stages of MultiQC execution are printed to the command line log.
  • New table config option only_defined_headers
    • Defaults to true, set to false to also show any data columns that are not defined as headers
    • Useful as allows table-wide defaults to be set with column-specific overrides
  • New module key allowed for config.extra_fn_clean_exts and config.fn_clean_exts
    • Means you can limit the action of a sample name cleaning pattern to specific MultiQC modules (#905)

New Custom Content features

  • Improve support for HTML files - now just end your HTML filename with _mqc.html
    • Native handling of HTML snippets as files, no MultiQC config or YAML file required.
    • Also with embedded custom content configuration at the start of the file as a HTML comment.
  • Add ability to group custom-content files into report sections
    • Use the new parent_id, parent_name and parent_description config keys to group content together like a regular module (#1008)
  • Custom Content files can now be configured using custom_data, without giving search patterns or data
    • Allows you to set descriptions and nicer titles for images and other 'blunt' data types in reports (#1026)
    • Allows configuration of custom content separately from files themselves (tsv, csv, txt formats) (#1205)

New Modules:

  • DRAGEN
    • Illumina Bio-IT Platform that uses FPGA for secondary NGS analysis
  • iVar
    • Added support for iVar: a computational package that contains functions broadly useful for viral amplicon-based sequencing.
  • Kaiju
    • Fast and sensitive taxonomic classification for metagenomics
  • Kraken
    • K-mer matching tool for taxonomic classification. Module plots bargraph of counts for top-5 hits across each taxa rank. General stats summary.
  • MALT
    • Megan Alignment Tool: Metagenomics alignment tool.
  • miRTop
    • Command line tool to annotate miRNAs with a standard mirna/isomir naming (mirGFF3)
    • Module started by @oneillkza and completed by @FlorianThibord
  • MultiVCFAnalyzer
    • Combining multiple VCF files into one coherent report and format for downstream analysis.
  • Picard - new submodules for QualityByCycleMetrics, QualityScoreDistributionMetrics & QualityYieldMetrics
  • Rockhopper
    • RNA-seq tool for bacteria, includes bar plot showing where features map.
  • Sickle
    • A windowed adaptive trimming tool for FASTQ files using quality
  • Somalier
    • Relatedness checking and QC for BAM/CRAM/VCF for cancer, DNA, BS-Seq, exome, etc.
  • VarScan2
    • Variant calling and somatic mutation/CNV detection for next-generation sequencing data

Module updates:

  • BISCUIT
    • Major rewrite to work with new BISCUIT QC script (BISCUIT v0.3.16+)
      • This change breaks backwards-compatability with previous BISCUIT versions. If you are unable to upgrade BISCUIT, please use MultiQC v1.8.
    • Fixed error when missing data in log files (#1101)
  • bcl2fastq
    • Samples with multiple library preps (i.e barcodes) will now be handled correctly (#1094)
  • BUSCO
    • Updated log search pattern to match new format in v4 with auto-lineage detection option (#1163)
  • Cutadapt
    • New bar plot showing the proportion of reads filtered out for different criteria (eg. too short, too many Ns) (#1198)
  • DamageProfiler
    • Removes redundant typo in init name. This makes referring to the module's column consistent with other modules when customising general stats table.
  • DeDup
    • Updates plots to make compatible with 0.12.6
    • Fixes reporting errors - barplot total represents mapped reads, not total reads in BAM file
    • New: Adds 'Post-DeDup Mapped Reads' column to general stats table.
  • FastQC
    • Fixed tooltip text in Sequence Duplication Levels plot (#1092)
    • Handle edge-case where a FastQC report was for an empty file with 0 reads (#1129)
  • FastQ Screen
    • Don't skip plotting % No Hits even if it's 0% (#1126)
    • Refactor parsing code. Avoids error with -0.00 %Unmapped (#1126)
    • New plot for Bisulfite Reads, if data is present
    • Categories in main plot are now sorted by the total read count and hidden if 0 across all samples
  • fgbio
    • New: Plot error rate by read position from ErrorRateByReadPosition
    • GroupReadsByUmi plot can now be toggled to show relative percents (#1147)
  • FLASh
    • Logs not reporting innie and outine uncombined pairs now plot combined pairs instead (#1173)
  • GATK
    • Made parsing for VariantEval more tolerant, so that it will work with output from the tool when run in different modes (#1158)
  • MTNucRatioCalculator
    • Fixed misleading value suffix in general stats table
  • Picard MarkDuplicates
    • Major change - previously, if multiple libraries (read-groups) were found then only the first would be used and all others ignored. Now, values from all libraries are merged and PERCENT_DUPLICATION and ESTIMATED_LIBRARY_SIZE are recalculated. Libraries can be kept as separate samples with a new MultiQC configuration option - picard_config: markdups_merge_multiple_libraries: False
    • Major change - Updated MarkDuplicates bar plot to double the read-pair counts, so that the numbers stack correctly. (#1142)
  • Picard HsMetrics
    • Updated large table to use columns specified in the MultiQC config. See docs. (#831)
  • Picard WgsMetrics
    • Updated parsing code to recognise new java class string (#1114)
  • QualiMap
    • Fixed QualiMap mean coverage calculation #1082, #1077
  • RSeqC
    • Support added for output from geneBodyCoverage2.py script (#844)
    • Single sample view in the "Junction saturation" plot now works with the toolbox properly (rename, hide, highlight) (#1133)
  • RNASeQC2
  • Samblaster
    • Improved parsing to handle variable whitespace (#1176)
  • Samtools
    • Removes hardcoding of general stats column names. This allows column names to indicate when a module has been run twice (#1076).
    • Added an observed over expected read count plot for idxstats (#1118)
    • Added additional (by default hidden) column for flagstat that displays number total number of reads in a bam
  • sortmerna
    • Fix the bug for the latest sortmerna version 4.2.0 (#1121)
  • sexdeterrmine
    • Added a scatter plot of relative X- vs Y-coverage to the generated report.
  • VerifyBAMID
    • Allow files with column header FREEMIX(alpha) (#1112)

Bug Fixes:

  • Added a new test to check that modules work correctly with --ignore-samples. A lot of them didn't:
    • Mosdepth, conpair, Qualimap BamQC, RNA-SeQC, GATK BaseRecalibrator, SNPsplit, SeqyClean, Jellyfish, hap.py, HOMER, BBMap, DeepTools, HiCExplorer, pycoQC, interop
    • These modules have now all been fixed and --ignore-samples should work as you expect for whatever data you have.
  • Removed use of shutil.copy to avoid problems with working on multiple filesystems (#1130)
  • Made folder naming behaviour of multiqc_plots consistent with multiqc_data
    • Incremental numeric suffixes now added if folder already exists
    • Plots folder properly renamed if using -n/--filename
  • Heatmap plotting function is now compatible with MultiQC toolbox hide and highlight (#1136)
  • Plot config logswitch_active now works as advertised
  • When running MultiQC modules several times, multiple data files are now created instead of overwriting one another (#1175)
  • Fixed minor bug where tables could report negative numbers of columns in their header text
  • Fixed bug where numeric custom content sample names could trigger a TypeError (#1091)
  • Fixed custom content bug HTML data in a config file would trigger a ValueError (#1071)
  • Replaced deprecated 'warn()' with 'warning()' of the logging module
  • Custom content now supports section_extra config key to add custom HTML after description.
  • Barplots with ymax set now ignore this when you click the Percentages tab.
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