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MultiQC Version 1.7
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@ewels ewels released this 21 Dec 20:07
v1.7
cab5a61

An early Christmas present for MultiQC users! 🎅🎁🎄

Many thanks to everyone who has contributed to this release. Happy Christmas and a very happy new year!

New Modules:

  • BISCUIT
    • BISuilfite-seq CUI Toolkit
    • Module written by @zwdzwd
  • DamageProfiler
    • A tool to determine ancient DNA misincorporation rates.
    • Module written by @apeltzer
  • FLASh
    • FLASH (Fast Length Adjustment of SHort reads)
    • Module written by @pooranis
  • MinIONQC
    • QC of reads from ONT long-read sequencing
    • Module written by @ManavalanG
  • phantompeakqualtools
    • A tool for informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data.
    • Module written by @chuan-wang
  • Stacks
    • A software for analyzing restriction enzyme-based data (e.g. RAD-seq). Support for Stacks >= 2.1 only.
    • Module written by @remiolsen

Module updates:

  • AdapterRemoval
    • Handle error when zero bases are trimmed. See #838.
  • Bcl2fastq
    • New plot showing the top twenty of undetermined barcodes by lane.
    • Informations for R1/R2 are now separated in the General Statistics table.
    • SampleID is concatenate with SampleName because in Chromium experiments several sample have the same SampleName.
  • deepTools
    • New PCA plots from the plotPCA function (written by @chuan-wang)
    • New fragment size distribution plots from bamPEFragmentSize --outRawFragmentLengths (written by @chuan-wang)
    • New correlation heatmaps from the plotCorrelation function (written by @chuan-wang)
    • New sequence distribution profiles around genes, from the plotProfile function (written by @chuan-wang)
    • Reordered sections
  • Fastp
    • Fixed bug in parsing of empty histogram data. See #845.
  • FastQC
    • Refactored Per Base Sequence Content plots to show original underlying data, instead of calculating it from the page contents. Now shows original FastQC base-ranges and fixes 100% GC bug in final few pixels. See #812.
    • When including a FastQC section multiple times in one report, the summary progress bars now behave as you would expect.
  • FastQ Screen
    • Don't hide genomes in the simple plot, even if they have zero unique hits. See #829.
  • InterOp
    • Fixed bug where read counts and base pair yields were not displaying in tables correctly.
    • Number formatting for these fields can now be customised in the same way as with other modules, as described in the docs
  • Picard
    • InsertSizeMetrics: You can now configure to what degree the insert size plot should be smoothed.
    • CollectRnaSeqMetrics: Add warning about missing rRNA annotation.
    • CollectRnaSeqMetrics: Add chart for counts/percentage of reads mapped to the correct strand.
    • Now parses VariantCallingMetrics reports. (Similar to GATK module's VariantEval.)
  • phantompeakqualtools
    • Properly clean sample names
  • Trimmomatic
    • Updated Trimmomatic module documentation to be more helpful
    • New option to use filenames instead of relying on the command line used. See #864.

New MultiQC Features:

  • Embed your custom images with a new Custom Content feature! Just add _mqc to the end of the filename for .png, .jpg or .jpeg files.
  • Documentation for Custom Content reordered to make it a little more sane
  • You can now add or override any config parameter for any MultiQC plot! See the documentation for more info.
  • Allow table_columns_placement config to work with table IDs as well as column namespaces. See #841.
  • Improved visual spacing between grouped bar plots

Bug Fixes:

  • Custom content no longer clobbers col1_header table configs
  • The option --file-list that refers to a text file with file paths to analyse will no longer ignore directory paths
  • Sample name directory prefixes are now added after cleanup.
  • If a module is run multiple times in one report, it's CSS and JS files will only be included once (default template)
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