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MultiQC Version 1.12
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@ewels ewels released this 08 Feb 22:14
v1.12
4aede39

Version 1.12 of MultiQC brings with it a modest number of new modules, a few new core features and a swathe of bugfixes and general improvements. I hope that everyone continues to find it useful! You can see the full changes in this release here: v1.11...v1.12

Special thanks to the 13 people who had their first MultiQC contributions in this release:

New Contributors

✨ MultiQC - new features

  • Added option to customise default plot height in plot config (#1432)
  • Added --no-report flag to skip report generation (#1462)
  • Added support for priting tool DOI in report sections (#1177)
  • Added support for --custom-css-file / config.custom_css_files option to include custom CSS in the final report (#1573)
  • New plot config option labelSize to customise font size for axis labels in flat MatPlotLib charts (#1576)
  • Added support for customising table column names (#1255)

🔨 MultiQC - updates

  • MultiQC now skips modules for which no files were found - gives a small performance boost (#1463)
  • Improvements for running MultiQC in a Python environment, such as a Jupyter Notebook or script
    • Fixed logger bugs when calling multiqc.run multiple times by removing logging file handlers between calls (#1141)
    • Init/reset global state between runs (#1596)
  • Added commonly missing functions to several modules (#1468)
  • Wrote new script to check for the above function calls that should be in every module (.github/workflows/code_checks.py), runs on GitHub actions CI
  • Make table Conditional Formatting work at table level as well as column level. (#761)
  • CSS Improvements to make printed reports more attractive / readable (#1579)
  • Fixed a problem with numeric filenames (#1606)
  • Fixed nasty bug where line charts with a categorical x-axis would take categories from the last sample only (#1568)
  • Ignore any files called multiqc_data.json (#1598)
  • Check that the config path_filters is a list, convert to list if a string is supplied (#1539)

🎁 New Modules

  • CheckQC
    • A program designed to check a set of quality criteria against an Illumina runfolder
  • pbmarkdup
    • Mark duplicate reads from PacBio sequencing of an amplified library
  • WhatsHap
    • WhatsHap is a software for phasing genomic variants using DNA sequencing reads

🌟 Module feature additions

  • BBMap
    • Added handling for qchist output (#1021)
  • bcftools
    • Added a plot with samplewise number of sites, Ts/Tv, number of singletons and sequencing depth (#1087)
  • Mosdepth
    • Added mean coverage #1566
  • NanoStat
    • Recognize FASTA and FastQ report flavors (#1547)

🐛 Module updates

  • BBMap
    • Correctly handle adapter stats files with additional columns (#1556)
  • bclconvert
    • Handle change in output format in v3.9.3 with new Quality_Metrics.csv file (#1563)
  • bowtie
    • Minor update to handle new log wording in bowtie v1.3.0 (#1615)
  • CCS
    • Tolerate compound IDs generated by pbcromwell ccs in the general statistics (#1486)
    • Fix report parsing. Update test on attributes ids (#1583)
  • Custom content
    • Fixed module failing when writing data to file if there is a / in the section name (#1515)
    • Use filename for section header in files with no headers (#1550)
    • Sort custom content bargraph data by default (#1412)
    • Always save custom content data to file with a name reflecting the section name. (#1194)
  • DRAGEN
    • Fixed bug in sample name regular expression (#1537)
  • Fastp
    • Fixed % pass filter statistics (#1574)
  • FastQC
    • Fixed several bugs occuring when FastQC sections are skipped (#1488, #1533)
    • Clarify general statistics table header for length
  • goleft/indexcov
    • Fix ZeroDivisionError if no bins are found (#1586)
  • HiCPro
    • Better handling of errors when expected data keys are not found (#1366)
  • Lima
    • Move samples that have been renamed using --replace-names into the General Statistics table (#1483)
  • miRTrace
    • Replace hardcoded RGB colours with Hex to avoid errors with newer versions of matplotlib (#1263)
  • Mosdepth
    • Fixed issue #1568
    • Fixed a bug when reporting per contig coverage
  • Picard
    • Update ExtractIlluminaBarcodes to recognise more log patterns in newer versions of Picard (#1611)
  • Qualimap
    • Fix ZeroDivisionError in QM_RNASeq and skip genomic origins plot if no aligned reads are found (#1492)
  • QUAST
    • Clarify general statistics table header for length
  • RSeQC
    • Fixed minor bug in new TIN parsing where the sample name was not being correctly cleaned (#1484)
    • Fixed bug in the junction_saturation submodule (#1582)
    • Fixed bug where empty files caused tin submodule to crash (#1604)
    • Fix bug in read_distribution for samples with zero tags (#1571)
  • Sambamba
    • Fixed issue with a change in the format of output from sambamba markdup 0.8.1 (#1617)
  • Skewer
    • Fix ZeroDivisionError if no available reads are found (#1622)
  • Somalier
    • Plot scaled X depth instead of mean for Sex plot (#1546)
  • VEP
    • Handle table cells containing - instead of numbers (#1597)

Contributors

yanick, maleasy, and 11 other contributors
Assets 2
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