Skip to content

MultiQC Version 1.15
Compare
Choose a tag to compare
@ewels ewels released this 04 Aug 22:02
v1.15
183d526
This commit was signed with the committer鈥檚 verified signature.
ewels Phil Ewels
SSH Key Fingerprint: 2vJRTr18pF9TOa8Stz1soprPmuVQ/KDdA3vECX6DaDg Learn about vigilant mode.

Big speedup in file search step

This release of MultiQC introduces speed improvements to the file search (~5-7x fold improvement) 馃帀

One way it does this is by limiting the number of lines loaded by each search pattern. For the vast majority of users, this should have no effect except faster searches. However, in some edge cases it may introduce some breaking changes. Hypothetically, for example:

  • If you concatenate log files from multiple tools
  • If you have a custom plugin module that we haven't tested

See the troubleshooting docs for more information.

MultiQC updates

  • Refactor file search for performance improvements (#1904)
  • Bump log_filesize_limit default (to skip large files in the search) from 10MB to 50MB.
  • Table code now tolerates lambda function calls with bad data (#1739)
  • Beeswarm plot now saves data to multiqc_data, same as tables (#1861)
  • Don't print DOI in module if it's set to an empty string.
  • Don't sort table headers alphabetically if we don't have an OrderedDict - regular dicts are fine in Py3 (#1866)
  • New back-end to preview + deploy the new website when the docs are edited.
  • Fixed a lot of broken links in the documentation from the new website change in structure.

New Modules

  • Librarian
    • A tool to predict the sequencing library type from the base composition of a supplied FastQ file.

Module updates

  • Cell Ranger
    • Bugfix: avoid multiple KeyError exceptions when parsing Cell Ranger 7.x web_summary.html (#1853, #1871)
  • DRAGEN
    • Restored functionality to show target BED coverage metrics (#1844)
    • Update filename pattern in RNA quant metrics (#1958)
  • filtlong
    • Handle reports from locales that use . as a thousands separator (#1843)
  • HUMID
    • Fix bug that prevent HUMID stats files from being parsed (#1856)
  • Mosdepth
    • Fix data not written to mosdepth_cumcov_dist.txt and mosdepth_cov_dist.txt (#1868)
    • Update documentation with new file {prefix}.mosdepth.summary.txt (#1868)
    • Fill in missing values for general stats table (#1868)
    • Include mosdepth/summary file paths in multiqc_sources.txt (#1868)
    • Enable log switch for Coverage per contig plot (#1868)
    • Fix y-axis scaling for Coverage distribution plot (#1868)
    • Handle case of intermediate missing coverage x-values in the *_dist.txt file causing a distorted Coverage distribution plot (#1960)
  • Picard
    • WgsMetrics: Fix wrong column label (#1888)
    • HsMetrics: Add missing field descriptions (#1928)
  • Porechop
    • Don't render bar graphs if no samples had any adapters trimmed (#1850)
    • Added report section listing samples that had no adapters trimmed
  • RSeQC
    • Fix ZeroDivisionError error for bam_stat results when there are 0 reads (#1735)
  • UMI-tools
    • Fix bug that broke the module with paired-end data (#1845)
Assets 2