MultiQC: summarize analysis results for multiple tools and samples in a single report

MultiQC new features Rewrote the Dockerfile to build multi-arch images (amd64 + arm), run through a non-privileged user and build tools for non precompiled python binaries (#1541, #1541) Add a new lint test to check that colour scale names are valid (#1835) Update github actions to run tests on a single module if it is the only file affected by the PR (#915) Add CI testing for Python 3.10 and 3.11 Optimize line-graph generation to remove an n^2 loop (#1668) Parsing output file column headers is much faster. MultiQC code cleanup Remove Python 2-3 compatability from __future__ imports Remove unused #!/usr/bin/env python hashbangs from module files Add new code formatting tool isort to standardise the order and formatting of Python module imports Add Pycln pre-commit hook to remove unused imports MultiQC updates Bugfix: Make config.data_format work again (#1722) Bump minimum version of Jinja2 to >=3.0.0 (#1642) Disable search progress bar if running with --quiet or --no-ansi (#1638) Allow path filters without full paths by trying to prefix analysis dir when filtering (#1308) Fix sorting of table columns with text values Don't crash if a barplot is given an empty list of categories (#1540) New logos! MultiQC is now developed and maintained at Seqera Labs. Updated logos and email addresses accordingly. New Modules Anglerfish A tool designed to assess pool balancing, contamination and insert sizes of Illumina library dry runs on Oxford Nanopore data. BBDuk Combines most common data-quality-related trimming, filtering, and masking operations via kmers into a single high-performance tool. Cell Ranger Works with data from 10X Genomics Chromium. Processes Chromium single cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. New MultiQC module parses Cell Ranger quality reports from VDJ and count analysis DIAMOND A high-throughput program for aligning DNA reads or protein sequences against a protein reference database. DRAGEN-FastQC Illumina Bio-IT Platform that uses FPGA for accelerated primary and secondary analysis Finally merged the epic 2.5-year-old pull request, with 3.5k new lines of code. Please report any bugs you find! Filtlong A tool for filtering long reads by quality. GoPeaks GoPeaks is used to call peaks in CUT&TAG/CUT&RUN datasets. HiFiasm A haplotype-resolved assembler for accurate Hifi reads HUMID HUMID is a tool to quickly and easily remove duplicate reads from FastQ files, with or without UMIs. mOTUs Microbial profiling through marker gene (MG)-based operational taxonomic units (mOTUs) Nextclade Tool that assigns clades to SARS-CoV-2 samples Porechop A tool for finding and removing adapters from Oxford Nanopore reads PRINSEQ++ PRINSEQ++ is a C++ of prinseq-lite.pl program for filtering, reformating or trimming genomic and metagenomic sequence data. UMI-tools Work with Unique Molecular Identifiers (UMIs) / Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes. Module updates Bcftools stats Bugfix: Do not show empty bcftools stats variant depth plots (#1777) Bugfix: Avoid exception when PSC nMissing column is not present (#1832) BclConvert Handle single-end read data correctly when setting cluster length instead of always assuming paired-end reads (#1697) Handle different R1 and R2 read-lengths correctly instead of assuming they are the same (#1774) Handle single-index paired-end data correctly Added a config option to enable the creation of barplots with undetermined barcodes (create_unknown_barcode_barplots with False as default) (#1709) BUSCO Update BUSCO pass/warning/fail scheme to be more clear for users Bustools Show median reads per barcode statistic Custom content Create a report even if there's only Custom Content General Stats there Attempt to cooerce line / scatter x-axes into floats so as not to lose labels (#1242) Multi-sample line-graph TSV files that have no sample name in row 1 column 1 now use row 1 as x-axis labels (#1242) fastp Add total read count (after filtering) to general stats table (#1744) Don't crash for invalid JSON files (#1652) FastQC Report median read-length for fastqc in addition to mean (#1745) Kaiju Don't crash if we don't have any data for the top-5 barplot (#1540) Kallisto Fix ZeroDivisionError when a sample has zero reads (#1746) Kraken Fix duplicate heatmap to account for missing taxons (#1779) Make heatmap full width Handle empty kreports gracefully (#1637) Fix regex error with very large numbers of unclassified reads (#1639) malt Fixed division by 0 in malt module (#1683) miRTop Avoid KeyError - don't assume all fields present in logs (#1778) Mosdepth Don't pad the General Stats table with zeros for missing data (#1810) Picard HsMetrics: Allow custom columns in General Stats too, with HsMetrics_genstats_table_cols and HsMetrics_genstats_table_cols_hidden Qualimap Added additional columns in general stats for BamQC results that displays region on-target stats if region bed has been supplied (hidden by default) (#1798) Bugfix: Remove General Stats rows for filtered samples (#1780) RSeQC Update geneBody_coverage to plot normalized coverages using a similar formula to that used by RSeQC itself (#1792) Sambamba Markdup Catch zero division in sambamba markdup (#1654) Samtools Added additional column for flagstat that displays percentage of mapped reads in a bam (hidden by default) (#1733) VEP Don't crash with ValueError if there are zero variants (#1681)Please consider citing MultiQC if you use it in your analysis