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MultiQC Version 1.6
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@ewels ewels released this 04 Aug 00:06
v1.6
1a8e205

Some of these updates are thanks to the efforts of people who attended the NASPM 2018 MultiQC hackathon session. Thanks to everyone who attended!

New Modules:

  • fastp
    • An ultra-fast all-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...)
    • Module started by @florianduclot and completed by @ewels
  • hap.py
    • Hap.py is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets
    • Module written by @tsnowlan
  • Long Ranger
    • Works with data from the 10X Genomics Chromium. Performs sample demultiplexing, barcode processing, alignment, quality control, variant calling, phasing, and structural variant calling.
    • Module written by @remiolsen
  • miRTrace
    • A quality control software for small RNA sequencing data.
    • Module written by @chuan-wang

Module updates:

  • BCFtools
  • BBMap
    • Support added for BBDuk kmer-based adapter/contaminant filtering summary stats (@boulund
  • FastQC
    • New read count plot, split into unique and duplicate reads if possible.
    • Help text added for all sections, mostly copied from the excellent FastQC help.
    • Sequence duplication plot rescaled
  • FastQ Screen
    • Samples in large-sample-number plot are now sorted alphabetically (@hassanfa
  • MACS2
    • Output is now more tolerant of missing data (no plot if no data)
  • Peddy
    • Background samples now shown in ancestry PCA plot (@roryk)
    • New plot showing sex checks versus het ratios, supporting unknowns (@oyvinev)
  • Picard
    • New submodule to handle ValidateSamFile reports (@cpavanrun)
    • WGSMetrics now add the mean and standard-deviation coverage to the general stats table (hidden) (@cpavanrun)
  • Preseq
    • New config option to plot preseq plots with unique old coverage on the y axis instead of read count
    • Code refactoring by @vladsaveliev
  • QUAST
    • Null values (-) in reports now handled properly. Bargraphs always shown despite varying thresholds. (@vladsaveliev)
  • RNA-SeQC
    • Don't create the report section for Gene Body Coverage if no data is given
  • Samtools
    • Fixed edge case bug where MultiQC could crash if a sample had zero count coverage with idxstats.
    • Adds % proper pairs to general stats table
  • Skewer
    • Read length plot rescaled
  • Tophat
    • Fixed bug where some samples could be given a blank sample name (@lparsons)
  • VerifyBamID
    • Change column header help text for contamination to match percentage output (@chapmanb)

New MultiQC Features:

  • New config option remove_sections to skip specific report sections from modules
  • Add path_filters_exclude to exclude certain files when running modules multiple times. You could previously only include certain files.
  • New exclude_* keys for file search patterns
    • Have a subset of patterns to exclude otherwise detected files with, by filename or contents
  • Command line options all now use mid-word hyphens (not a mix of hyphens and underscores)
    • Old underscore terms still maintained for backwards compatibility
  • Flag --view-tags now works without requiring an "analysis directory".
  • Removed Python dependency for enum34 (@boulund)
  • Columns can be added to General Stats table for custom content/module.
  • New --ignore-symlinks flag which will ignore symlinked directories and files.
  • New --no-megaqc-upload flag which disables automatically uploading data to MegaQC

Bug Fixes

  • Fix path_filters for top_modules/module_order configuration only selecting if all globs match. It now filters searches that match any glob.
  • Empty sample names from cleaning are now no longer allowed
  • Stop prepend_dirs set in the config from getting clobbered by an unpassed CLI option (@tsnowlan)
  • Modules running multiple times now have multiple sets of columns in the General Statistics table again, instead of overwriting one another.
  • Prevent tables from clobbering sorted row orders.
  • Fix linegraph and scatter plots data conversion (sporadically the incorrect ymax was used to drop data points) (@cpavanrun)
  • Adjusted behavior of ceiling and floor axis limits
  • Adjusted multiple file search patterns to make them more specific
    • Prevents the wrong module from accidentally slurping up output from a different tool. By @cpavanrun (see PR #727)
  • Fixed broken report bar plots when -p/--export-plots was specified (see issue #801)
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