MultiQC/MultiQC v1.20

MultiQC version 1.20

on GitHub

Highlights

New plotting library

MultiQC v1.20 comes with totally new plotting code for MultiQC reports. This is a huge change to the report output. We've done our best to maintain feature parity with the previous plotting code, but please do let us know if you spot any bugs or changes in behaviour by creating a GitHub issue.

This change comes with many improvements and new features, and paves the way for more in the future. To find out more, read the associated blog post.

For now, you can revert to the previous plotting code by using the highcharts report template (multiqc --template highcharts). This will be removed in v1.21.

Note that there are several plotting configuration options which have been removed:

• click_func
• cursor
• tt_percentages (use tt_suffix: "%")
• Bar plot:
  • use_legend (automatically hidden if there is only 1 category)
• Line plot:
  • labelSize
  • xDecimals, yDecimals (automatic if all values can be cast to int)
  • xLabelFormat, yLabelFormat (use tt_label)
  • pointFormat
• Heatmap:
  • datalabel_colour
  • borderWidth

Moved GitHub and docker repositories

The v1.20 release is also the first release we've had since we moved the MultiQC repositories. Please note that the code is now at MultiQC/MultiQC (formerly ewels/MultiQC) and the same for the Docker repository. The GitHub repo should automatically redirect, but it's still good to update any references you may have.

MultiQC updates

• Support Plotly as a new backend for plots (#2079)
  • The default template now uses Plotly for all plots
  • Added a new plot type violin (replaces beeswarm)
  • Moved legacy Highcharts/Matplotlib code under an optional template highcharts
    (#2292)
• Move GitHub repository to MultiQC organisation (#2243)
• Update all GitHub actions to their latest versions (#2242)
• Update docs to work with Astro 4 (#2256)
• Remove unused dependency on future library (#2258)
• Fix incorrect scale IDs caught by linting (#2272)
• Docs: fix missing v prefix in docker image tags (#2273)
• Unicode file reading errors: attempt to skip non-unicode characters (#2275)
• Heatmap: check if value is numeric when calculating min and max (#2276)
• Add filesearch_file_shared config option, remove unnecessary per-module shared flags in search patterns (#2227)
• Use alternative method to walk directory using pathlib (#2277)
• Export config.output_dir in MegaQC JSON (#2287)
• Drop support for module tags (#2278)
• Pin Pillow package, wrap add_logo in try-except (#2312)
• Custom content: support multiple datasets (#2291)
• Configuration: fix reading config.output_fn_name and --filename (#2314)

New modules

• Bamdst (#2161)
  • Bamdst is a lightweight tool to stat the depth coverage of target regions of bam file(s).
• MetaPhlAn (#2262)
  • MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
• MEGAHIT (#2222)
  • MEGAHIT is an ultra-fast and memory-efficient NGS assembler
• Nonpareil (#2215)
  • Estimate metagenomic coverage and sequence diversity.

Module updates

• Bcftools: order variant depths plot categories (#2289)
• Bcftools: add missing self.ignore_samples in stats (#2288)
• BCL Convert: add index, project names to sample statistics and calculate mean quality for lane statistics. (#2261)
• BCL Convert: fix duplicated yield for 3.9.3+ when the yield is provided explicitly in Quality_Metrics (#2253)
• BCL Convert: handle samples with zero yield (#2297)
• Bismark: fix old link in Bismark docs (#2252)
• Bismark: fix old link in docs (#2252)
• Cutadapt: support JSON format (#2281)
• HiFiasm: account for lines with no asterisk (#2268)
• HUMID: add cluster statistics (#2265)
• mosdepth: add additional summaries to general stats #2257 (#2257)
• Picard: fix using multiple times in report: do not pass module.anchor to self.find_log_files (#2255)
• QualiMap: address NBSP as thousands separators (#2282)
• Seqera Platform CLI: updates for v0.9.2 (#2248)
• Seqera Platform CLI: handle failed tasks (#2286)

New Contributors

• @a-detiste made their first contribution in #2258
• @mbeavitt made their first contribution in #2268
• @almahans made their first contribution in #2262
• @kmlhpk made their first contribution in #2273
• @studioph made their first contribution in #2277
• @vsmalladi made their first contribution in #1503

Full Changelog: v1.19...v1.20