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MultiQC v1.31

MultiQC

Adding new module for Xenium analysis, 10x Genomics Xenium spatial transcriptomics quality control report.

The parquet format is stable since 1.29, renaming the output file from BETA-multiqc.parquet to multiqc.parquet.

New modules​

Feature updates and improvements​

  • Add return_html parameter for programmatic HTML access (#3304)
  • File search optimization: avoid reading files when contents exclusion patterns are not provided (#3312)
  • Rename BETA-multiqc.parquet to multiqc.parquet (#3332)

Fixes​

  • Scatter plot: fix hiding dots by legend click (#3321)
  • Plots: set unique series label for each plot type (#3330)
  • Fix bulk sample renaming buttons (#3300)
  • Fix config flag types in schema (#3318)
  • Ignore pyc files when copying html files (#3320)

Module updates​

  • Picard tools: enhance QualityByCycleMetrics to support original quality scores (#3307)
  • STAR: improve module color scheme for better accessibility (#3305, #3306)
  • Sequali: support insert size metrics (#3303)
  • Missing modules to general stats: Busco, CheckM, CheckM2, GTDB-Tk (#3289)
  • cells2stats: add support for optical pooled screening output (#3277)
  • fastp: add before-filtering mean r1/r2 length to general stats (#3280)
  • Cutadapt: improve sample name extraction for stdin input (#3333)

Module fixes​

  • bases2fastq: fix index error (#3328)
  • Picard: fix VariantCallingMetrics to support sample renaming (#3298)
  • fastp: fix sample naming for paired-end reads (#3302)
  • bcftools: fix singleton count calculation to include indels (#3295)
  • CheckM2: column spelling fix (#3283)
  • Bulk replace deprecated hide_empty with hide_zero_cats (#3296)

Infrastructure and packaging​

  • WASM workaround: if write_parquet not supported by polars, write a CSV file (#3309)
  • Add Claude instructions (#3301)
  • Add Claude review action (#3299)