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MultiQC Version 1.8
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@ewels ewels released this 20 Nov 15:59
v1.8
acbc04a

A huge release, this one has been a long time coming. Due to @ewels being away on paternity leave for over six months it was very delayed and has been nearly a year in the making! During that time there has been 344 commits with 3,370 lines of code added and 1,194 deletions by 19 contributors. That's a lot of changes.

Highlights include:

  • Finally removing the annoying YAML warning
  • Six new modules, and many large updates to existing modules
  • Code restructuring allowing MultiQC to be imported into Python environments and easier running on Windows
  • Lots of tiny bug fixes all over the place.

Enjoy the update! And I promise I'll try not to make everyone wait so long for the next release...

Full changelog

New Modules:

  • fgbio
    • Process family size count hist data from GroupReadsByUmi
  • biobambam2
    • Added submodule for bamsormadup tool
    • Totally cheating - it uses Picard MarkDuplicates but with a custom search pattern and naming
  • SeqyClean
    • Adds analysis for seqyclean files
  • mtnucratio
    • Added little helper tool to compute mt to nuclear ratios for NGS data.
  • mosdepth
    • fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing
  • SexDetErrmine
    • Relative coverage and error rate of X and Y chromosomes

Module updates:

  • bcl2fastq
    • Added handling of demultiplexing of more than 2 reads
    • Allow bcl2fastq to parse undetermined barcode information in situations when lane indexes do not start at 1
  • BBMap
    • Support for scafstats output marked as not yet implemented in docs
  • DeDup
    • Added handling clusterfactor and JSON logfiles
  • damageprofiler
    • Added writing metrics to data output file.
  • DeepTools
    • Fixed Python3 bug with int() conversion (#1057)
    • Handle varied TES boundary labels in plotProfile (#1011)
    • Fixed bug that prevented running on only plotProfile files when no other deepTools files found.
  • fastp
    • Fix faulty column handling for the after filtering Q30 rate (#936)
  • FastQC
    • When including a FastQC section multiple times in one report, the Per Base Sequence Content heatmaps now behave as you would expect.
    • Added heatmap showing FastQC status checks for every section report across all samples
    • Made sequence content individual plots work after samples have been renamed (#777)
    • Highlighting samples from status - respect chosen highlight colour in the toolbox (#742)
  • FastQ Screen
    • When including a FastQ Screen section multiple times in one report, the plots now behave as you would expect.
  • GATK
    • Refactored BaseRecalibrator code to be more consistent with MultiQC Python style
    • Handle zero count errors in BaseRecalibrator
  • HiC Explorer
    • Fixed bug where module tries to parse QC_table.txt, a new log file in hicexplorer v2.2.
  • HTSeq
    • Fixed bug where module would crash if a sample had zero reads (#1006)
  • LongRanger
    • Added support for the LongRanger Align pipeline.
  • miRTrace
    • Fixed bug where a sample in some plots was missed. (#932)
  • Peddy
    • Fixed bug where sample name cleaning could lead to error. (#1024)
    • All plots (including Het Check and Sex Check) now hidden if no data
  • Picard
    • Modified OxoGMetrics.py so that it will find files created with GATK CollectMultipleMetrics and ConvertSequencingArtifactToOxoG.
  • QoRTs
    • Fixed bug where --dirs broke certain input files. (#821)
  • Qualimap
    • Added in mean coverage computation for general statistics report
    • Creates now tables of collected data in multiqc_data
  • RNA-SeQC
    • Updated broken URL link
  • RSeQC
    • Fixed bug where Junction Saturation plot when clicking a single sample was mislabelling the lines.
    • When including a RSeQC section multiple times in one report, clicking Junction Saturation plot now behaves as you would expect.
    • Fixed bug where exported data in multiqc_rseqc_read_distribution.txt files had incorrect values for _kb fields (#1017)
  • Samtools
    • Utilize in-built read_count_multiplier functionality to plot flagstat results more nicely
  • SnpEff
    • Increased the default summary csv file-size limit from 1MB to 5MB.
  • Stacks
    • Fixed bug where multi-population sum stats are parsed correctly (#906)
  • TopHat
    • Fixed bug where TopHat would try to run with files from Bowtie2 or HiSAT2 and crash
  • VCFTools
    • Fixed a bug where tstv_by_qual.py produced invalid json from infinity-values.
  • snpEff
    • Added plot of effects

New MultiQC Features:

  • Added some installation docs for windows
  • Added some docs about using MultiQC in bioinformatics pipelines
  • Rewrote Docker image
    • New base image czentye/matplotlib-minimal reduces image size from ~200MB to ~80MB
    • Proper installation method ensures latest version of the code
    • New entrypoint allows easier command-line usage
  • Support opening MultiQC on websites with CSP script-src 'self' with some sha256 exceptions
    • Plot data is no longer intertwined with javascript code so hashes stay the same
  • Made config.report_section_order work for module sub-sections as well as just modules.
  • New config options exclude_modules and run_modules to complement -e and -m cli flags.
  • Command line output is now coloured by default 🌈 (use --no-ansi to turn this off)
  • Better launch comparability due to code refactoring by @KerstenBreuer and @ewels
    • Windows support for base multiqc command
    • Support for running as a python module: python -m multiqc .
    • Support for running within a script: import multiqc and multiqc.run('/path/to/files')
  • Config option custom_plot_config now works for bargraph category configs as well (#1044)
  • Config table_columns_visible can now be given a module namespace and it will hide all columns from that module (#541)

Bug Fixes:

  • MultiQC now ignores all .md5 files
  • Use SafeLoader for PyYaml load calls, avoiding recent warning messages.
  • Hide multiqc_config_example.yaml in the test directory to stop people from using it without modification.
  • Fixed matplotlib background colour issue (@epakarin - #886)
  • Table rows that are empty due to hidden columns are now properly hidden on page load (#835)
  • Sample name cleaning: All sample names are now truncated to their basename, without a path.
    • This includes for regex and replace (before was only the default truncate).
    • Only affects modules that take sample names from file contents, such as cutadapt.
    • See #897 for discussion.
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