ewels/MultiQC: MultiQC Version 1.11

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

• 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.

• 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

• 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)

• 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)

• 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)