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MultiQC Version 1.16
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@ewels ewels released this 22 Sep 14:35
v1.16
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Highlight: Reporting software versions

New in v1.16 - software version information can now automatically parsed from log output where available, and added to MultiQC in a standardised manner. It's shown in the MultiQC report next to section headings and in a dedicated report section, as well as being saved to multiqc_data. Where version information is not available in logs, it can be submitted manually by using a new special file type with filename pattern *_mqc_versions.yml. There's the option of representing groups of versions, useful for a tool that uses sub-tools, or pipelines that want to report version numbers per analysis step.

There are a handful of new config scopes to control behaviour: software_versions, skip_versions_section, disable_version_detection, versions_table_group_header.
See the documentation for more (writing modules, supplying stand-alone)

Huge thanks to @pontushojer for the contribution (#1927). This idea goes way back to issue #290, made in 2016! 🎉

MultiQC updates

  • Removed simplejson unused dependency (#1973)
  • Give config custom_plot_config priority over column-specific settings set by modules
  • When exporting plots, make a more clear error message for unsupported FastQC dot plot (#1976)
  • Fixed parsing of plot_type: "html" data in json custom content
  • Replace deprecated pkg_resources
  • Fix the module groups configuration for modules where the namespace is passed explicitly to general_stats_addcols. Namespace is now always appended to the module name in the general stats (2037).
  • Do not call sys.exit() in the multiqc.run() function, to avoid breaking interactive environments. #2055
  • Fixed the DOI exports in multiqc_data to include more than just the MultiQC paper (#2058)
  • Fix table column color scaling then there are negative numbers (1869)
  • Export plots as static images and data in a ZIP archive. Fixes the issue when only 10 plots maximum were downloaded due to the browser limitation.

New Modules

  • Bakta
    • Rapid and standardized annotation of bacterial genomes, MAGs & plasmids.
  • mapDamage
    • mapDamage2 is a computational framework written in Python and R, which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
  • Sourmash
    • Quickly search, compare, and analyze genomic and metagenomic data sets.

Module updates

  • BcfTools
    • Stats: fix parsing multi-sample logs (#2052)
  • Custom content
    • Don't convert sample IDs to floats (#1883)
  • DRAGEN
    • Make DRAGEN module use fn_clean_exts instead of hardcoded file names. Fixes working with arbitrary file names (#1994)
  • FastQC:
    • fix UnicodeDecodeError when parsing fastqc_data.txt: try latin-1 or fail gracefully (#2024)
  • Kaiju:
    • Fix UnboundLocalError on outputs when Kanju was run with the -e flag (#2023)
  • Kraken
    • Parametrize top-N through config (#2060)
    • Fix bug where ranks incorrectly assigned to tabs (#1766).
  • Mosdepth
    • Add X/Y relative coverage plot, analogous to the one in samtools-idxstats (#1978)
    • Added the perchrom_fraction_cutoff option into the config to help avoid clutter in contig-level plots
    • Fix a bug happening when both region and global coverage histograms for a sample are available (i.e. when mosdepth was run with --by, see mosdepth docs). In this case, data was effectively merged. Instead, summarise it separately and add a separate report section for the region-based coverage data.
    • Do not fail when all input samples have no coverage (#2005).
  • NanoStat
    • Support new format (#1997).
  • RSeQC
    • Fix max() arg is an empty sequence error (#1985)
    • Fix division by zero on all-zero input (#2040)
  • Samtools
    • Stats: fix "Percent Mapped" plot when samtools was run with read filtering (#1972)
  • Qualimap
    • BamQC: Include % On Target in General Stats table (#2019)
  • WhatsHap
    • Bugfix: ensure that TSV is only split on tab character. Allows sample names with spaces (#1981)

New Contributors

Full Changelog: v1.15...v1.16

Contributors

lindenb, antass, and 8 other contributors
Assets 2
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