ewels/MultiQC: MultiQC Version 1.12

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: https://github.com/ewels/MultiQC/compare/v1.11...v1.12

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

<details> <summary>New Contributors</summary> * @HofLucien made their first contribution in https://github.com/ewels/MultiQC/pull/1486 * @jchorl made their first contribution in https://github.com/ewels/MultiQC/pull/1578 * @bjohnnyd made their first contribution in https://github.com/ewels/MultiQC/pull/1489 * @schorlton made their first contribution in https://github.com/ewels/MultiQC/pull/1567 * @MatthiasZepper made their first contribution in https://github.com/ewels/MultiQC/pull/1584 * @g-pacheco made their first contribution in https://github.com/ewels/MultiQC/pull/1587 * @paulstretenowich made their first contribution in https://github.com/ewels/MultiQC/pull/1605 * @yanick made their first contribution in https://github.com/ewels/MultiQC/pull/1595 * @MillironX made their first contribution in https://github.com/ewels/MultiQC/pull/1594 * @sguizard made their first contribution in https://github.com/ewels/MultiQC/pull/1593 * @maleasy made their first contribution in https://github.com/ewels/MultiQC/pull/1552 * @TomaszSuchan made their first contribution in https://github.com/ewels/MultiQC/pull/1271 * @massiddamt made their first contribution in https://github.com/ewels/MultiQC/pull/1021 </details>✨ 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)