MultiQC Version 1.1

New Modules:

• BioBloom Tools
  • Create Bloom filters for a given reference and then to categorize sequences
• Conpair
  • Concordance and contamination estimator for tumor–normal pairs
• Disambiguate
  • Bargraph displaying the percentage of reads aligning to two different reference genomes.
• Flexbar
  • Flexbar is a tool for flexible barcode and adapter removal.
• HISAT2
  • New module for the HISAT2 aligner.
  • Made possible by updates to HISAT2 logging by @infphilo (requires --new-summary HISAT2 flag).
• HOMER
  • Support for summary statistics from the findPeaks tool.
• Jellyfish
  • Histograms to estimate library complexity and coverage from k-mer content.
  • Module written by @vezzi
• MACS2
  • Summary of redundant rate from MACS2 peak calling.
• QoRTs
  • QoRTs is toolkit for analysis, QC and data management of RNA-Seq datasets.
• THetA2
  • THeTA2 (Tumor Heterogeneity Analysis) estimates tumour purity and clonal / subclonal copy number.

Module updates:

• BCFtools
  • Option to collapse complementary changes in substitutions plot, useful for non-strand specific experiments (thanks to @vladsaveliev)
• Bismark
  • M-Bias plots no longer show read 2 for single-end data.
• Custom Content
  • New option to print raw HTML content to the report.
• FastQ Screen
  • Fixed edge-case bug where many-sample plot broke if total number of reads was less than the subsample number.
  • Fixed incorrect logic of config option fastqscreen_simpleplot (thanks to @daler)
  • Organisms now alphabetically sorted in fancy plot so that order is nonrandom (thanks to @daler)
  • Fixed bug where %No Hits was missed in logs from recent versions of FastQ Screen.
• HTSeq Counts
  • Fixed but so that module still works when --additional-attr is specified in v0.8 HTSeq above (thanks to @nalcala)
• Picard
  • CollectInsertSize: Fixed bug that could make the General Statistics Median Insert Size value incorrect.
  • Fixed error in sample name regex that left trailing ] characters and was generally broken (thanks to @jyh1 for spotting this)
• Preseq
  • Improved plots display (thanks to @vladsaveliev)
• Qualimap
  • Only calculate bases over target coverage for values in General Statistics. Should give a speed increase for very high coverage datasets.
• QUAST
  • Module is now compatible with runs from MetaQUAST (thanks to @vladsaveliev)
• RSeQC
  • Changed default order of sections
  • Added config option to reorder and hide module report sections

New MultiQC features:

• If a report already exists, execution is no longer halted.
  • _1 is appended to the filename, iterating if this also exists.
  • -f/--force still overwrites existing reports as before
  • Feature written by @Hammarn
• New ability to run modules multiple times in a single report
  • Each run can be given different configuration options, including filters for input files
  • For example, have FastQC after trimming as well as FastQC before trimming.
  • See the relevant documentation for more instructions.
• New option to customise the order of report sections
  • This is in addition / alternative to changing the order of module execution
  • Allows one module to have sections in multiple places (eg. Custom Content)
• Tables have new column options floor, ceiling and minRange.
• Reports show warning if JavaScript is disabled
• Config option custom_logo now works with file paths relative to config file directory and cwd.

Bug Fixes:

• Table headers now sort columns again after scrolling the table
• Fixed buggy table header tooltips
• Base clean_s_name function now strips excess whitespace.
• Line graphs don't smooth lines if not needed (number of points < maximum number allowed)
• PDF output now respects custom output directory.