changelog
     version 1.18.02
        - Added SYSargs2 to the main vignette
        
     version 1.18.01
        - Fixed bug in loadWorkflow function - class==Workflow
        
     version 1.17.11
        - Fixed bug in loadWorkflow function - class==Workflow
	    - Added 'more.args' to clusterRun function (Updated help file)
 
     version 1.17.10
        - Updated links in vignettes

     version 1.17.9
        - Support Rstudio Server moduleload in runCommandline

     version 1.17.8
        - Fixed typo in "subsetWF" and "writeTargetsout" functions

     version 1.17.7
        - Added SYSargs2 and SYSargs2Pipe classes and Methods
        - Added "loadWorkflow", "renderWF", "subsetWF", "output_update", "targets.as.df" functions
        - Added respective help files for all functions and classes above
        - Added folder inst/extdata/cwl/*
	    - Updated alignStats, clusterRun, runCommandline, and writeTargetsout functions and the corresponding help files (Allowing SYSargs2 object)
	    - Transferred "inst/extdata/slides" and "inst/extdata/ignette_archive/" to systemPipeRdata package
	    - Workflows templates - size reduced. Full version in systemPipeRdata package
	    - Unused figures removed 

     version 1.17.6
        - Small bug fix in overLapper function 

     version 1.17.5
        - Updated clusterRun function by recent batchtools package
        - Updated help files related to clusterRun function examples
        - Update runCommanline function to handle the stop in the module function (system with no Environment Modules)
        - New templates to SGE, Slurm and Torque clusters

     version 1.17.4
        - Bugfix in vignettes (systemPipeRNAseq, systemPipeVARseq, and systemPipeChIPseq)

     version 1.17.3
        - Switched all vignettes to R markdown (*.Rmd) followed by small updates

     version 1.17.2
        - Added "ImmunoOncology" to biocViews in Description File
    
    version 1.17.1
        - Improved vignette instructions
    
    version 1.15.3
        - Fixed typo in vignette

    version 1.15.1
        - Updated description file 
    
    version 1.11.3
        - Fixed duplicated commits 
        - Adopted to new default setting of maxgap in findOverlaps
        - Minor formatting improvements
    
    version 1.11.2
        - Support for passing on several environmental variables in moduleload
    
    version 1.11.1
        - Fixed gene set naming problem in GOCluster_Report

    version 1.9.2
        - Added make_bam argument to runCommandline
    
    version 1.7.0 - 1.9.1
        - vignette updates

    version 1.5.8 - 1.5.9
        - bugfix in seeFastqPlot caused by recent change in ggplot2
        - fix in fstats component of seeFastq

    version 1.5.6 - 1.5.7
        - vignette updates

    version 1.5.5
        - fixed extendylim in plotfeatureCoverage()
        - fixed error in featureCoverage when txdb/grl was created from gff with scaffolds not containing any genes

    version 1.5.0 - 1.5.4
        - doc updates
        - git mirror setup
        - fixed genFeatures for txdb instance from makeTxDbFromUCSC()
        - fixed genFeatures for empty range sets

    version 1.3.44 - 1.3.50
        - added predORF
        - added scaleRanges
        - optimized performance of scaleRanges
        - vignette updates
        - translational efficiency modeling with DESeq2

    version 1.3.35 - 1.3.43
        - added featureCoverage and plotfeatureCoverage
        - vignette updates
    
    version 1.3.31 - 1.3.35
        - added Ribo-Seq function: genFeature
        - added Ribo-Seq functions: featuretypeCounts and plotfeaturetypeCounts
        
    version 1.3.23 - 1.3.30
        - vignette updates
        - updated ChIP-Seq workflow
    
    version 1.3.21 - 1.3.22
        - added writeTargetsRef and mergeBamByFactor
    
    version 1.3.17 - 1.3.10
        - Converted main vignette to R Markdown
        - Instructions to download sample data via systemPipeRdata
        - Fix for missing systemPipeRdata on build system
        - Fix to get correct name of HTML page on Bioc page

    version 1.3.16
        - Fixed minor bug in runCommandline

    version 1.3.14 - 1.3.15
        - Fixed PE support in preprocessReads
    
    version 1.3.13
        - Included gsnap and VariantTools examples in vignette
    
    version 1.3.8 - 1.3.12
        - vignette updates 
    
    version 1.3.7
        - added sample Makefile 
    
    version 1.3.4 - 1.3.6
        - vignette updates 
    
    version 1.3.3
        - updated readComp 
        - corrected typo for systemArgs when NULL is assigned to sysma
    
    version 1.3.2
        - fixed path to BatchJob's log file location when symbolic links are used
    
    version 1.1.16
        - added functions for variant filtering and annotation
    
    version 1.1.15
        - support for GATK and BCFtools
    
    version 1.1.12-1.1.14
        - vignette/man updates
    
    version 1.1.11
        - added DESeq2 support
    
    version 1.1.9-1.1.10
        - vignette/man updates
    
    version 1.1.8
        - added preprocessReads function
    
    version 1.1.7
        - support for R-based software generating input/output files
        - support for pipelines with several system command steps
    
    version 1.1.6
        - added new *.param files
    
    version 1.1.5
        - vignette updates
    
    version 1.1.4
        - updated vennPlot

    version 1.1.3
        - added functions: overLapper, vennPlot and olBarplot
        - eliminated warning in seeFastq
    
    version 1.1.2
        - documentation update

    version 0.99.0 - 1.1.1
        - initial version on Bioconductor