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Published February 8, 2022 | Version v1.13
Software Open

MultiQC: summarize analysis results for multiple tools and samples in a single report

Authors/Creators

Description

MultiQC updates
  • Major spruce of the command line help, using the new rich-click package
  • Drop some of the Python 2k compatability code (eg. custom requirements)
  • Improvements for running MultiQC in a Python environment, such as a Jupyter Notebook or script
    • Fixed bug raised when removing logging file handlers between calls that arose when configuring the root logger with dictConfig (#1643)
  • Added new config option custom_table_header_config to override any config for any table header
  • Fixed edge-case bug in custom content where a description that doesn't terminate in . gave duplicate section descriptions.
  • Tidied the verbose log to remove some very noisy statements and add summaries for skipped files in the search
  • Add timezone to time in reports
  • Add nix flake support
  • Added automatic tweet about new releases
Module updates
  • AdapterRemoval
    • Finally merge a fix for counts of reads that are discarded/collapsed (#1647)
  • VEP
    • Fixed bug when General Statistics have a value of - (#1656)
  • Custom content
    • Only set id for custom content when id not set by metadata (#1629)
    • Fix bug where module wouldn't run if all content was within a MultiQC config file (#1686)
    • Fix crash when info isn't set (#1688)
  • Nanostat
    • Removed HTML escaping of special characters in the log to fix bug in jinja2 v3.10 removing jinja2.escape() (#1659)
    • Fix bug where module would crash if input does not contain quality scores (#1717)
  • Pangolin
    • Updated module to handle outputs from Pangolin v4 (#1660)
  • Somalier
    • Handle zero mean X depth in Sex plot (#1670)
  • Fastp
    • Include low complexity and too long reads in filtering bar chart
  • miRTop
    • Fix module crashing when ref_miRNA_sum is missing in file. (#1712)
    • Fix module crashing due to zero division (#1719)
  • FastQC
    • Fixed error when parsing duplicate ratio when there is nan values in the report. (#1725)

Notes

Please consider citing MultiQC if you use it in your analysis.

Files

ewels/MultiQC-v1.13.zip

Files (2.4 MB)

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Additional details

Related works

Is supplement to
https://github.com/ewels/MultiQC/tree/v1.13 (URL)