MultiQC version 1.19

Highlights

An early Christmas present 🎁 Happy holidays everyone! 🎄

This release is mostly bugfixes and minor additions, whilst we lay the groundwork for some bigger updates coming in the new year. Still, there are plenty of goodies in here. Enjoy!

See the full changes in this release here: v1.18...v1.19

MultiQC updates

• Add missing table id in DRAGEN modules, and require id in plot configs in strict mode (#2228)
• Config table_columns_visible and table_columns_name: support flat config and table_id as a group (#2191)
• Add sort_samples: false config option for bar graphs (#2210)
• Upgrade the jQuery tablesorter plugin to v2 (#1666)
• Refactor pre-Python-3.6 code, prefer f-strings over .format() calls (#2224)
• Allow specifying default sort columns for tables with defaultsort (#1667)
• Create CODE_OF_CONDUCT.md (#2195)
• Add .cram to sample name cleaning defaults (#2209)

MultiQC bug fixes

• Re-add run into the multiqc namespace (#2202)
• Fix the "square": True flag to scatter plot to actually make the plot square (#2189)
• Fix running with the --no-report flag (#2212)
• Fix guessing custom content plot type: do not assume first row of a bar plot data are sample names (#2208)
• Fix detection of changed specific module in Changelog CI (#2234)

Module updates

• BCLConvert: fix mean quality, fix count-per-lane bar plot (#2197)
• deepTools: handle missing data in plotProfile (#2229)
• Fastp: search content instead of file name (#2213)
• GATK: square the BaseRecalibrator scatter plot (#2189)
• HiC-Pro: add missing search patterns and better handling of missing data (#2233)
• Kraken: fix UnboundLocalError (#2230)
• Kraken: fixed column keys in genstats (#2205)
• QualiMap: fix BamQC for global-only stats (#2207)
• Picard: add more search patterns for MarkDuplicates, including MarkDuplicatesSpark (#2226)
• Salmon: add library_types, compatible_fragment_ratio, strand_mapping_bias to the general stats table (#1485)

New Contributors

• @gsmashd made their first contribution in #2205
• @kclem made their first contribution in #2235

Full Changelog: v1.18...v1.19