changelog

changelog
    version 1.99.12
	- Update systemPipeRdata vignette
	
    version 1.99.10
	- remove old script from gatk.
	
    version 1.99.9
	- batchtools.slurm.tmpl --> requires partition specification on the resources list.
	- avoid x11 for chipseq template.
	
    version 1.99.8
	- Cleanup NAMESPACE
	- Set up actions: If vignettes/*Rmd are updated, automatically inst/extdata/workflows/*/*.Rmd and
			inst/extdata/workflows/*/*.R, inst/extdata/workflows/*/*.html are updated. 
			Also, the individual packages are updated on the SP organization.
	
    version 1.23.6/7
	- RIBO-seq template
	
    version 1.23.3/4
	- RNA-seq template
	- Chip-seq template
	- VAR-seq template
	
    version 1.23.2
	- RNA-seq template
	
    version 1.23.1
	- trim_galore cwl files
	
    version 1.21.4
	- fastqc cwl files
	
    version 1.21.2/3
	- New RNA-seq
	
    version 1.21.1
	- Updated CWL param files
	
    version 1.19.10
	- Vignette RIBO-seq
	
    version 1.19.9
	- Vignette ChIP-seq
	
    version 1.19.6
	- Removed .batchtools.conf.R file from .Rbuildignore
	
    version 1.19.5
	- Copied the .batchtools.conf.R file to Github WF templates
	
    version 1.19.4
	- Small updates, version up
	
    version 1.19.3
	- Exported `getSubsetReads` function

    version 1.19.2
	- Added `getSubsetReads` function
	- Added new cwl files
	- Updated vignette
	
    version 1.19.1
	- Updated systemPipeRNAseq and systemPipeVARseq vignettes
	
    version 1.17.4
	- Updated systemPipeR* vignettes
	
    version 1.17.3
	- Fixed typo systemPipeRdata vignette   
	
     version 1.17.2
        - Updated systemPipeRdata vignette
        - Updated help files
        - New function: "availableWF" 
        
     version 1.17.1
        - Fixed typo on the vignettes
        
     version 1.15.5
        - Updating the order of the workflows on Bioc webpage
        
     version 1.15.3
        - Added workflow "NEW" -  basic structure of the SYS_project
	    - Updated 'genWorkenvir' function and help file (Added new arguments allowing to download/install and create a specific project from GitHub package)
        
     version 1.15.2
        - Fixed message=FALSE load library vignette
        
     version 1.15.1
        - Updated the vignettes 'inst/extdata/workflows/*"

     version 1.13.5
        - Added "cwl/*" files:
            - GATK/*
            - bcftools/*
            - varseq/*
        - Updated vignettes: 'varseq'

     version 1.13.4
        - Updated vignettes
        - Added "cwl/*" files:
            - MACS2/*
            - annotate_peaks/*
            - count_rangesets/*
            - mergeBamByFactor/*
            - rundiff/*

    version 1.13.3
	- Updated Vignettes
	
    version 1.13.2
	- Added the param/docopt.R/*
	- Added the data with valid Id Names
	
    version 1.13.1
	- Added new *cwl files
	
    version 1.11.5
	- Removed PDF from vignettes directory

    version 1.11.5
	- Added default *.html

    version 1.11.4
	- Added systemPipeR vignettes (*.pdf)

    version 1.11.3
	- Added systemPipeR vignettes

    version 1.11.2
	- Updated systemPipeRdata vignette   
        
    version 1.11.1
	- Updated 'genWorkenvir' function and help file (Added new argument allowing to download a specific template file/version) 
	- Makefile update (support for .Rmd)
	- Removed old .tmpl files and added new batchtools files
        - Bibtex update (in the workflows and systemPipeRdata vignette)
	- Updated all the vignettes in the workflow (removed old .Rnw templates)
	- Removed all the .pdf figures in the workflows subdirecty
	- Updated systemPipeRdata vignette
    
    version 1.9.1
        - Kallisto *.param added
    
    version 1.5.1
        - Switched all vignettes to R markdown (*.Rmd)
        
    version 1.3.7 - 1.5.0
        - various updates
    
    version 1.3.6
        - Support for SLURM 
        - R markdown template for RNA-Seq
    
    version 1.3.5
        - added trim_galore.param

    version 1.3.4
        - Fixed path problem for Windows

    version 1.3.3
        - Started to change workflow scripts to R markdown with support to render to both HTML or PDF. 
          So far this has been done only for RIBO-Seq workflow. Others will be added later.
        - Added argument to include bam files in results directory
    
    version 1.1.1
        - RIBO-Seq vignette update
    
    version 0.99.1
        - initial package commit