Change log

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

[0.10.0] -- 2021-07-20

Changed

  • Make refgenie optional
  • Use looper refgenie populate plugin to integrate refgenie
  • Update docs to reflect changes to refgenie requirement and installation
  • Fix file.path in reducePeaks() and take sample name argument
  • Update blacklist reduce peaks step
  • Rework CLI arguments to be fully explicit
  • Update settings in R
  • Update dockerfile to most recent refgenie usage and R package changes
  • Reduce smaller file resource requests

Added

  • Add assets descriptions and how to obtain to docs
  • Add script to check native, conda, and container-based installs

[0.9.16] -- 2021-05-18

Changed

  • Updated consensus peak documentation
  • Reintroduced single container images and corresponding documentation
  • Added minimum score and minimum overlap parameters to consensus peak generation
  • Restore use of original F-seq as optional peak caller
  • Updated peak calling using F-seq, HOMER, and HMMRATAC
  • Updated PEPATACr package to rely less on PEPs within functions
  • Move stats summary generation to R and outside of looper table

[0.9.15] -- 2021-03-03

Added

  • Add PEP, count table, consensus peak generation documentation
  • Add license

Changed

  • Fix documentation page links
  • Updated argument types case
  • Added ability to adjust minimum sample count when creating consensus peaks

[0.9.14] -- 2021-02-05

Changed

  • Update F-Seq to F-Seq2
  • Add the option to install using conda
  • Add script for easing installation of seqOutBias
  • Use https for PEP schema; list alternative local PEP schema approach

[0.9.13] -- 2020-12-02

Changed

  • Fix recovery mode for modified fastq repairing checks

[0.9.12] -- 2020-12-01

Changed

  • Update bulker crate and version

[0.9.11] -- 2021-03-04

Changed

  • Fixed error in order of argument terms for _remove_adapters()

Added

  • Added documentation for using custom adapters

[0.9.10] -- 2020-09-28

Changed

  • Changed looper pypi term
  • Updated documentation to reflect companion software updates

[0.9.9] -- 2020-08-28

Changed

  • Improve clarity of trimmed reads reporting

[0.9.8] -- 2020-06-16

Changed

  • Fix summarizer file path construction
  • Add minimum version requirements to required software
  • Update uninformative adapter read calculation
  • Update example output
  • Update pause index calculation to be inflexible to depth
  • Fix cFRiF y-axis
  • Update cutadapt calculations to newer versions of cutadapt
  • Update resource defaults
  • Update requirement base versions
  • Update schema

[0.9.7] -- 2020-05-26

Added

  • Create assets summary for samples and project
  • Add optional scaling of signal tracks

Changed

  • Update to PEP 2.0 standard
  • Update docs and examples

[0.9.6] -- 2020-03-31

Changed

  • Fixed refgenie bowtie2 index assignment

[0.9.5] -- 2020-03-26

Changed

  • Updated FRiF calculation to only account for the count column
  • Updated FRiF calculation to check if results are empty

[0.9.4] -- 2020-03-25

Changed

  • Updated bowtie2 index checks to be in line with refgenie updates

[0.9.3] -- 2020-03-25

Changed

  • Added checks for correct value return on cutadapt report checks

[0.9.2] -- 2020-03-25

Changed

  • Updated refgenconf use from get_asset() to seek()
  • Added check for bowtie2_index asset naming

[0.9.1] -- 2020-02-27

Added

  • Report project counts table as a summary object
  • Clean up additional uncommonly used downstream files

Changed

  • Use bulker for container usage
  • Update R install process
  • Correct FastQC object reporting
  • Updated logic for recover mode
  • Default max length trimming is now none
  • Change nomenclature regarding FRiF/PRiF plots
  • Change TSS score nomenclature

[0.9.0] -- 2020-02-20

Added

  • Add a how-to guide for configuring UMI settings

Changed

  • Update mRNA contamination plots display properties to be more readable
  • Update pause index plots to default to log10 histograms and update their display properties
  • Use paper samples as the default output examples in the docs

[0.8.9] -- 2020-02-11

Changed

  • Corrected Pct_reads_too_short calculation
  • Updated mRNA and PI plots to plot on same axis across sample
  • Updated minimum acceptable read length
  • Produce both signal track types

[0.8.8] -- 2020-02-04

Changed

  • Updated degradation ratio calculation for PE data
  • Corrected Pct_reads_too_short to be percent not fraction

[0.8.7] -- 2020-02-04

Changed

  • Updated degradation ratio calculation for SE data
  • Fixed report_fastq to properly handle SE, non UMI data

[0.8.6] -- 2020-01-28

Changed

  • Update FRiF calculation to optionally follow a priority ranked method
  • Update how adapter insertion distributions are plotted to be the same for SE or PE data
  • Make cutadapt the default for adapter removal
  • Streamline the use of Refgenie assets
    • Refgenie manages pause indicies
    • Refgenie manages feature annotations
    • Refgenie manages assets for mRNA contamination
    • Refgenie manages seqOutBias required suffixerator indicies
  • Change pause index and mRNA contamination plots to histograms

Added

  • Add PRiF plot
  • Require FLASH tool
  • Produce sample level gene counts file as output
  • Generate project level counts table including all samples X gene counts
  • Report degradation metric for library quality
  • Add BiocProject integration

[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