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MultiQC Version 1.11
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@ewels ewels released this 05 Jul 07:13
v1.11
5206e04

A summer release for MultiQC 🥳 🏖️ Many thanks to everyone who has contributed!

MultiQC new features

  • New interactive slider controls for controlling heatmap colour scales (#1427)
  • Added new --replace-names / config sample_names_replace option to replace sample names during report generation
  • Added use_filename_as_sample_name config option / --fn_as_s_name command line flag (#949, #890, #864, #998, #1390)
    • Forces modules to use the log filename for the sample identifier, even if the module usually takes this from the file contents
    • Required a change to the clean_s_name() function arguments. All core MultiQC modules updated to reflect this.
    • Should be backwards compatible for custom modules. To adopt new behaviour, supply f instead of f["root"] as the second argument.
    • See the documenation for details: Using log filenames as sample names and Custom sample names.

MultiQC updates

  • Make the module crash tracebacks much prettier using rich
  • Refine the cli log output a little (nicely formatted header line + drop the [INFO])
  • Added docs describing tools for downstream analysis of MultiQC outputs.
  • Added CI tests for Python 3.9, pinned networkx package to >=2.5.1 (#1413)
  • Added patterns to config.fn_ignore_paths to avoid error with parsing installation dir / singularity cache (#1416)
  • Print a log message when flat-image plots are used due to sample size surpassing plots_flat_numseries config (#1254)
  • Fix the mqc_colours util function to lighten colours even when passing categorical or single-length lists.
  • Bugfix for Custom Content, using YAML configuration (eg. section headers) for images should now work

New Modules

  • BclConvert
    • Tool that converts / demultiplexes Illumina Binary Base Call (BCL) files to FASTQ files
  • Bustools
    • Tools for working with BUS files
  • ccs
    • Generate highly accurate single-molecule consensus reads from PacBio data
  • GffCompare
    • GffCompare can annotate and estimate accuracy of one or more GFF files compared with a reference annotation.
  • Lima
    • The PacBio Barcode Demultiplexer
  • NanoStat
    • Calculate various statistics from a long read sequencing datasets
  • ODGI
    • Optimized dynamic genome/graph implementation
  • Pangolin
    • Added MultiQC support for Pangolin, the tool that determines SARS-CoV-2 lineages
  • Sambamba Markdup
    • Added MultiQC module to add duplicate rate calculated by Sambamba Markdup.
  • Snippy
    • Rapid haploid variant calling and core genome alignment.
  • VEP
    • Added MultiQC module to add summary statistics of Ensembl VEP annotations.
    • Handle error from missing variants in VEP stats file. (#1446)

Module feature additions

  • Cutadapt
    • Added support for linked adapters #1329]
    • Parse whether trimming was 5' or 3' for Lengths of Trimmed Sequences plot where possible
  • Mosdepth
    • Include or exclude contigs based on patterns for coverage-per-contig plots
  • Picard
    • Add support for CollectIlluminaBasecallingMetrics, CollectIlluminaLaneMetrics, ExtractIlluminaBarcodes and MarkIlluminaAdapters (#1336)
    • New insertsize_xmax configuration option to limit the plotted maximum insert size for InsertSizeMetrics
  • Qualimap
    • Added new percentage coverage plot in QM_RNASeq (#1258)
  • RSeQC
    • Added a long-requested submodule to support showing the TIN (Transcript Integrity Number) (#737)

Module updates

  • biscuit
    • Duplicate Rate and Cytosine Retention tables are now bargraphs.
    • Refactor code to only calculate alignment statistics once.
    • Fixed bug where cytosine retentions values would not be properly read if in scientific notation.
  • bcl2fastq
    • Added sample name cleaning so that prepending directories with the -d flag works properly.
  • Cutadapt
    • Plot filtered reads even when no filtering category is found (#1328)
    • Don't take the last command line string for the sample name if it looks like a command-line flag (#949)
  • Dragen
    • Handled MultiQC crashing when run on single-end output from Dragen (#1374)
  • fastp
    • Handle a ZeroDivisionError if there are zero reads (#1444)
  • FastQC
    • Added check for if overrepresented_sequences is missing from reports (#1281)
  • Flexbar
    • Fixed bug where reports with 0 reads would crash MultiQC (#1407)
  • Kraken
    • Handle a ZeroDivisionError if there are zero reads (#1440)
    • Updated search patterns to handle edge case (#1428)
  • Mosdepth
    • Show barplot instead of line graph for coverage-per-contig plot if there is only one contig.
  • Picard
    • RnaSeqMetrics - fix assignment barplot labels to say bases instead of reads (#1408)
    • CrosscheckFingerprints - fix bug where LOD threshold was not detected when invoked with "new" picard cli style. fixed formatting bug (#1414)
    • Made checker for comma as decimal separator in HsMetrics more robust (#1296)
  • qc3C
    • Updated module to not fail on older field names.
  • Qualimap
    • Fixed wrong units in tool tip label (#1258)
  • QUAST
    • Fixed typo causing wrong number of contigs being displayed (#1442)
  • Sentieon
    • Handled ZeroDivisionError when input files have zero reads (#1420)
  • RSEM
    • Handled ZeroDivisionError when input files have zero reads (#1040)
  • RSeQC
    • Fixed double counting of some categories in read_distribution bar graph. (#1457)
Assets 2