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MultiQC v1.26

MultiQC

Christmas release! 10 new modules, 11 improved modules, and a few core improvements.

Highlights​

  • Custom content: Allow quoting strings in CSV to prevent interpreting them as numbers (#3020)
  • Naturally sort samples in tables and bar plots (#2999)
  • Auto-save dynamic toolbox settings (#3001)
  • report.saved_raw_data is not preserved by default to save on memory footprint (#3010). You can enable it with preserve_module_raw_data: true in your config file.

New modules​

  • MosaiCatcher - tool for classifying strand states of each chromosome in each cell using a Hidden Markov Model (#1910)
  • ataqv - tool for assessing the quality of a genome using a broader set of marker genes (#3013)
  • telseq - a software that estimates telomere length from whole genome sequencing data (BAMs) (#2910)
  • Cell Ranger ARC - analysis of single cell expression or VDJ data produced by 10X Genomics (#2925)
  • GTDB-Tk - toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes (#2970)
  • Checkm - genome completeness and contamination based on the presence or absence of marker genes (#2990)
  • Checkm2: rapid, scalable and accurate tool for assessing microbial genome quality using machine learning (#2978)
  • Haplocheck - detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitchondrial content (#2933)
  • mgikit - demultiplexes FASTQ files from an MGI sequencing instrument (#3023)
  • Percolator - semi-supervised learning for peptide identification from shotgun proteomics datasets (#3011)

Module updates​

  • GATK BQSR: support Sentieon QualCal output (#3008)
  • Pychopper: add section with UMI barpot (#3024)
  • fastp: add overrepresented sequences plot and table (#3000)
  • RNA-SeqC: more metrics in general statistics table (#3017)
  • phantompeakqualtools: adjust minimum value to 1 for NSC coeff (#3021)
  • QualiMap RNASeq: add gen stats columns for exonic, intronic, intergenic, overlapping (#3018)
  • QualiMap BamQC: add general stats columns for dup rate, number of Ns, mapped paired reads (#2989)
  • DRAGEN: RNA quant metrics: support forward and reverse fragments in barplot (#3012)
  • Interop: remove "%" suffix for nan values (#2995)
  • Dedup: use a more specific search pattern (#2988)
  • Bclconvert: group samples and lanes, refactor (#2872)
  • Nanostat: new format: fix parsing sample names (#3007)

Feature updates and improvements​

  • Custom content: allow quoting strings in CSV (#3020)
  • Naturally sort samples in tables and bar plots (#2999)
  • Auto-save dynamic toolbox settings to session and to a file (#3001)
  • Support Python 3.13, drop 3.8 (#2862)
  • Add table tooltips about merged values in groupped samples (#3002)

Fixes​

  • Align order of lineplot categories across samples (#3033)

Optimization, refactoring, and typing​

  • Memory optimization: do not preserve saved_raw_data in modules, write directly to files instead (#3010)
  • Violin plot: add dt into Dataset objects instead of main_table_dt (#2968)

Infrastructure and packaging​

  • Add Cursor rules for module creation (#3025)
  • Fix docker build: remove docs from .dockerignore (#2994)
  • Add workflow to sync changelog with Seqera docs (#2993)
  • Docker build: add workflow_dispatch, do not push on pull_request (#2962)
  • Build and test Docker image in PRs (#2958)
  • Fix Docker CI for forks: skip login step (#2953)
  • Document bar plot's sort_samples (#3006)
  • Update ruff to 0.8.3 (#3029)
  • Add more tests for custom-content (#3028)
  • Add pytest ini options to pyproject.toml - to set default test targets (#3030)