ewels/MultiQC: MultiQC Version 1.6

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

• 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

• BCFtools
  • New plot showing SNP statistics versus quality of call from bcftools stats (@MaxUlysse and @Rotholandus)
• 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 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

• 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)