CHANGES IN VERSION 1.22
-----------------------

OVERVIEW

The following enhancements have been added to systemPipeR.

    - With the upgrades provided in this release, systemPipeR has become a much
      more generic data analysis workflow environment that is no longer limited 
      to analyzing just NGS data. Now it can be efficiently used for data analysis 
      tasks in many omics areas, including genomics, proteomics, metabolomics and drug discovery.
    - A workflow control class (SYSargsList) has been added allowing users to 
     manage multiple-step workflows from a single container. This way one can select 
     and execute multiple workflow steps with standard R subsetting syntax,
      e.g. runWF[1:3].
    - Various improvements have been added to systemPipeR’s new  command-line 
      interface including the recently introduced SYSargs2 class that supports 
      the Common Workflow Language (CWL).
    - Utilities have been added to visualize workflow designs and topologies with 
      different graphical layouts.
    - Improvements have been added to monitor the run status of workflows as well 
      as better tracking of warning and error messages. This includes the generation 
      of both scientific and technical status reports.



CHANGES IN VERSION 1.3
----------------------

OVERVIEW

    o systemPipeR is an R/Bioconductor package for building and running automated
      analysis workflows for a wide range of next generation sequence (NGS)
      applications. Important features include a uniform workflow interface
      across different NGS applications, automated report generation, and support
      for running both R and command-line software, such as NGS aligners or
      peak/variant callers, on local computers or compute clusters. Efficient
      handling of complex sample sets and experimental designs is facilitated by
      a consistently implemented sample annotation infrastructure.

    o The most important enhancements in the upcoming release of the package are 
      outlined below.  
    
NGS WORKFLOWS

    o Added new end-to-end workflows for 3 additional NGS application areas: 
        - Ribo-Seq and polyRibo-Seq 
        - ChIP-Seq
        - VAR-Seq
      The previous version of systemPipeR included only a complete workflow for
      RNA-Seq.

    o Added the data package 'systemPipeRdata' to generate systemPipeR workflow
      environments with a single command (genWorkenvir) containing all parameter
      files and sample data required to quickly test and run workflows. This
      change will also allow evaluation of much more code examples in the
      vignettes during the package build/test process than this was possible in
      the past. 

    o About 20 new functions have been added to the package. Some examples are:
        - Read pre-processor function with support for SE and PE reads
        - Parallelization option of detailed FASTQ quality reports
        - Read distribution plots across all features available in a 
          genome annotation (see ?featuretypeCounts) 
        - Visualization of coverage trends along transcripts summarized 
          for any number of transcripts (see ?featureCoverage)
        - Functionalities to predict uORFs/sORFs and to use them for expression profiling
        - Differential expression/binding analysis includes now DESeq2 as
          well as edgeR

    o Added param templates for additional command-line software including, but 
      not limited to: BWA-MEM, GATK, BCFtools, MACS2

    o Adoption of R Markdown for main vignette. Future plans are to provide for
      all workflows the report templates in both formats: Latex/PDF and
      R_Markdown/HTML.

WORFLOW FRAMEWORK

    o Simplified design of complex analysis workflows. Workflows can now include
      any number or combination of R and/or command-line steps

    o Improvements to workflow automation and parallelization on single
      machines and computer clusters. This also includes now many additional
      parallelization examples in the workflow vignettes.


