Change log

All notable changes to this project will be documented in this file.

[0.8.1] -- 2019-07-15

Changed

  • Fix fraction in feature calculation
  • Fix library complexity calculation for PE data
  • Require fastq_pair tool
  • Require cutadapt for SE processing

Added

  • Add QC plot for adapter insertion distribution

[0.8.0] -- 2019-07-10

Changed

  • Update pause index calculation and required annotation files
  • Update mRNA contamination required annotation files
  • Move fastq processing to separate function
  • Change handling of PE data
  • Update TSS profiling

Added

  • Add modified fastq_pair tool to handle PE data properly
  • Add pause index plotting
  • Add mRNA contamination calculation and plotting
  • Add fragment length distribution plotting for PE data

[0.7.3] -- 2019-06-13

Changed

  • Fix missing gt in container
  • Fix mappability bug with new refgenie

[0.7.2] -- 2019-06-13

Changed

  • Fix --new-start bug
  • Fix container libgsl library
  • Adjust seqOutBias usage and flexibility

[0.7.1] -- 2019-06-12

Changed

  • Update to new refgenie usage
  • Update container

[0.7.0] -- 2019-06-11

Changed

  • Fix multiple input file handling
  • Update preseq calculation and plotting and handle small samples
  • Fix TSS plotting and score calculation
  • Include bedtools in required software

Added

  • Add project level library complexity summarizer
  • Add docs
  • Add container
  • Add small test example

[0.6.0] -- 2019-06-04

Changed

  • Use PEPPRO R package for QC plotting and analysis
  • Default uses intermediate read files to produce a deduplicated and non-deduplicated aligned BAM file
  • Check for cutadapt version for multicore processing
  • Update bigWig production to be variable step formatted wig

Added

  • Handle GRO-seq data as input
  • Created and included a PEPPRO R package for standard functions
  • Add preseq requirement and plot library complexity curve
  • Calculate and report read depth
  • Calculate and report the percent of adapter contamination
  • Produce fraction of reads in features plot

[0.5.1] -- 2019-05-09

Changed

  • Simplify and clarify prealignment steps

Added

  • Perform a pre-check that all required tools are callable