changelog

changelog
    version 2.3.2
        - Environment Modules system -->  back to the previous version
        
    version 2.3.1
        - Fix style of R files
        - Improvement of runWF and renderLogs functions
        
    version 2.1.31
        - Update vignette.
        
    version 2.1.30
        - Environment Modules system > 4.0.0: new version. 
        
    version 2.1.28
        - Fix varseq bug
        
    version 2.1.25
        - Fix runWF --> logs
        - Adding final lines for renderReport function
        
    version 2.1.22
        - Updated help files
        
    version 2.1.20/21
        - Added trimbatch
        
    version 2.1.19
        - fix plotwf warning color 
        
    version 2.1.18
        - Added a new argument to countRangeset and runDiff functions
        - small fix for writeTargetsRef
        - small fix for getColumn and updateColumn
        
    version 2.1.17
        - small fix for read_SYSargsList
        
    version 2.1.16
        - Added a new argument to mergeBamByFactor function
        
    version 2.1.15
        - varseq functions argument deprecated
        - Added SE Replacement method (SYSargsList)
        - writeTargetsout and alignStats: small fix
        - symLink2bam: added named character vector alternative as input
        
    version 2.1.14
        - renderLogs: small fix for the Title
        
    version 2.1.13
        - Reorganized `SPRproject` function internal execution 
        
    version 2.1.12
        - Update SYSargsList man page
        - Exported 'addResources' method
        - Fixed a small bug yamlinput replacement method
        - Unexported "updateStatus<-" and "runInfo<-"
        - Fixing time when `resume = TRUE`
        
    version 2.1.11
        - Fixing message moduleload() windows system
        - renameStep accepts the same name
        - dependency replacement method accepts NA
        - SYSargsList accepts `targets = SE` object
        - Fixed log/SE path
        
    version 2.1.10
        - management and compute running option names
        
    version 2.1.9
        - Bug fixed pathInstance and runWF
        
    version 2.1.8
        - plotWF panel control options
        - runCommnadline bug fixed
        
    version 2.1.7
        - R code can be submitted to compute node - internal function
        
    version 2.1.6
        - Allows targets subset with runWF 
        - Improved running time when targets subset

    version 2.1.5
        - runWF remote option added
        
    version 2.1.4
        - runInfo Replacement method update
        
    version 2.1.3
        - yamlinput methods update
        
    version 2.1.2
        - preprocessReads updates
        
    version 2.1.1
        - runCommandline function: 
            - Fixed status/file.exists dataframe;
            - input_targets improved.
        - runWF function: run_step, ignore.dep and targets arguments added.
        
    version 1.99.32
        - Updated importWF, sal2bash and sal2rmd functions
        - Updated plotWF function

    version 1.99.31
        - Updated renderReport function

    version 1.99.30
        - allowing multiple steps dependency == NA
        - Fixed replaceStep

    version 1.99.29
        - cwlFilesUpdate function 

    version 1.99.28
        - Update package version

    version 1.27.27
        - After SPRproject(resume=TRUE), spr_importing option

    version 1.27.26
        - accepting 'input.results.path' to cwl description file

    version 1.27.24/1.27.25
        - Dependencies and global variables fixed

    version 1.27.23
        - Added new method: updateStatus<-
        - Added new slot to LineWise Class - runInfo
        - Added new arguments to LineWise function: 
            - run_step
            - run_session
        - Updated write_SYSargsList and read_SYSargsList
        - Removed LineWise slot: rmdPath. Info can be found on the files slot or still using the method 
        - Added random numbers to log files names + collect each R code steps logs

    version 1.27.22
        - slot runInfo updated
        - Updates Documentation
        - Minor fixes

    version 1.27.20/21
        - Updates Documentation
        - Minor fixes
        
    version 1.27.18/19
        - Updates Documentation
        - Minor fixes: infile1/infile2, alignStats
        - exporting write_SYSargsList
    
    version 1.27.17
        - Updates Documentation
        - Minor fixes
    
    version 1.27.16
        - Exported "sal2rmd" and "sal2bash"
    
    version 1.27.15
        - Updates Documentation
        - Minor fixes
    
    version 1.27.14
        - clusterRun()
    
    version 1.27.12
        - plotWF accepts empty sal + minor updates
        - alias tryCMD
    
    version 1.27.12
        - plotWF accepts empty sal + minor updates
       - alias tryCMD
        - New argument createParam (confirm=FALSE)
        - sal object with relative Paths
        - Improvements SPRproject: resume and restart
        - Bugs: runCommandLine and tryCMD
        - Bugs fixed: replaceSteps<- + improvements
        - Bug fixed: dependency in LineWise and SYSargsList functions
        - Documentation
        - Removed requirement of SampleName for loadWF
        - Internal functions: .checkSpecialChar; .cbindTargetsOutfiles; .checkInputVars

     version 1.27.11
        - Deprecated: getQsubargs and qsubRun functions
        - LineWise: help files and files organization
        - SYSargs2: help files and files organization
        - SYSargsList: help files and files organization
        - AllClasses and AllGenerics exclusive files
        
     version 1.27.10
        - plotWF() --> New design 
        - Forcing dependency argument
        - outfiles double check: the original location + New location in cases of dir=TRUE
        - Forcing 'targetsWF' and 'outfiles' columns names need to be unique
        - New method: updateColumn()
        - Updated varseq functions
        - importWF() and LineWise() improved
        - alignStats() improved
        - LineWise status Success --> skip
        - Documentation
        
     version 1.27.9
        - Renamed subsetOutfiles() to getColumn()
        - Added internal slot for SYSargs2 'internal_outfiles' -> This allows to keep the original output paths, important for the internal updates within runCommandline()
        - Internal validation for adding a new step improved 
        - importWF() improved
        - Force option for runCommandline() improved
        - Documentation
        
     version 1.27.8
        - Added viewEnvir() and copyEnvir(), stepName(), subsetOutfiles() methods
        - targetsheader(), SampleName() methods for SYSargsList 
        - SampleName() methods for SYSargs2
        - Improved subsetTargets() methods
        - Steps names needs to be unique.
        - Added output names at files slot at SYSargs2 obj
        - outfiles(sal) --> colnames from cwl file
        - progress bar for LineWise
        - runCommandline --> removed sample subfolder structure
        
     version 1.27.7
         - Added option to dir=T/F for each step
         - Fixed bugs to save and restart SYSargsList object
         - Added colors to status show method
        
     version 1.27.6
         - SYSargs2 updates:
             - status(): New Method and slot
             - Update show Method
         - SYSargsList updates: 
             - Rename slot projectInfo
             - runInfo(): New slot and Method
             - Removed sprconfig method/slot
             - Update statusWF() printing and replacement methods
             - show() method: more details
             - New methods: viewEnvir and copyEnvir
         - LineWise Upadates:
             - New slot/methods: status()
        - Update SPRproject, write_SYSargsList, read_SYSargsList, SYSargsList, runWF, renderReport, renderLogs, SYScreate functions
        - Major improvement in RunCommandline function

     version 1.27.5
         - check.output for SYSargsList
         - New Fct: cmdTool2wf
         - New Methods: subsetTargets; 
         - Improve SYSargsList Methods
         - SPRproject function (new internal design)
         - `+` method
         - LineWise Class and Methods
         - CWL templates path 
         - New unit tests
         - Vignettes
         
     version 1.27.4
         - R CMD build and check _R_CHECK_LENGTH_1_CONDITION_=verbose
     version 1.27.3
         - Adding createParamFiles, "writeParamFiles", "printParam", "subsetParam", "replaceParam", "renameParam", "appendParam", "updateWF", "SYSargsList" functions
         - Adding "cmdToCwl", "baseCommand", "sprconfig", "stepsWF", "statusWF", "dependency", "projectInfo", "targetsWF", "SEobj", "outfiles", "sysargslist", "appendStep<-", "replaceStep<-", "renameStep<-" methods
         - Updating SYSargs2 and SYSargsList class
        - Updating "loadWorkflow", "createWF", "output_update", "write.clt", "write.yml", "SYScreate", "runWF", "initWF"  functions
        - Adding systemPipeR_CWL.Rmd vignette
        
     version 1.27.2
         - Special case for Rscript
         
     version 1.27.1
         - Added unittest 
                  
     version 1.25.17
         - Fixed bug: 'symLink2bam()'
                  
     version 1.25.16
         - `module()` bug fix for RStudio Server
         - `plotfeaturetypeCounts()` and `plotfeaturetypeCounts()` --> `scale_x_discrete`
                  
     version 1.25.14
        - Clean message from `runCommandline()`
        - Fixed bug on `initWF()`
        - Updated Vignette
        - Printing message for `createWF()`
        - upgrade `runWF()`
                  
     version 1.25.13
         - Fixed `GO.db` dependency
         
     version 1.25.12
         - Fixed .Rbuildignore
         
     version 1.25.11
         - Added "cwl/*" files:
        - BUSCO/*
        - blast/*
        - bowtie2/bowtie2-mi/*
        - bwa/bwa-aln/*
        - bwa/bwa-mem-pe/*
        - bwa/bwa-mem-se/*
        - bwa/bwa-samse/*
        - cutadapt/*
        - fastqc/*
        - fastx_toolkit/*
        - gunzip/*
        - kallisto/*
        - picard/*
        - star/*
        - workflow-bwa-aln/*

     version 1.25.10
        - `moduleload` updated help file
        - Added `check.output` function
        - Fixed `renderWF` fct (`.renderWFsingle`) to accept stdout
        - `tryCL` deals with `fastqc` commandline test
        - Added `lfcShrink` option to `run_DESeq2` function
        - Allow `alignStats` fct accepts different `subset="FileName1"` from targets
        
     version 1.25.9
        - Added print behavior to `write.cwl` and `write.yml`
        - Fixed bug `genFeatures()`
        - Vignette update
        
     version 1.25.8
        - Reducing package dependency
        - Reducing 'Undefined global functions or variables'
        
     version 1.25.7
        - Updated URL
        - Organized functions files: "SYSargsList and SYSargs2" classes --> R/AllClasses2.R
        - Removed 'SYSargs2Pipe-class'
        
     version 1.25.6
        - Function wrapper showDT(DT::datatable)
        - Fixed bug: 'symLink2bam()'
        - Vignette update
        
     version 1.25.5
        - Updating 'renderWF' and 'config.param' functions
        
     version 1.25.4
        - Help file update in 'creadWF.Rd'
        
     version 1.25.3
        - Adding new Methods: 'addAssay' and 'addMetadata': Extension accessor for SummarizedExperiment object 
        - Adding New function: 'SPRdata()'
        
     version 1.25.2
        - NAMESPACE
        
     version 1.25.1
        - Version bump
        
     version 1.23.9
        - Vignette update
        
     version 1.23.8
        - Converting myEnvModules S3 class to S4 class
        - Adding new Methods: "available_modules", "loaded_modules", "default_modules", "modulecmd"
        
     version 1.23.7
        - Fixing: "warning in read.delim(... comment = "#"): partial argument match of 'comment' to 'comment.char'"
        
     version 1.23.6
        - Importing selectively functions from the `grid` package. Avoiding conflict with `Biostrings` package: "replacing previous import 'Biostrings::pattern' by 'grid::pattern'"
        
     version 1.23.5
        - Warning fixed: [yaml::read_yaml(eval.expr=TRUE)] more details here: https://github.com/viking/r-yaml/issues/47
        
     version 1.23.4
        - Fixed bug: '.makeBam'
        
     version 1.23.3
        - moduleload function BugFix: [IIGB_MODULES >> HPCC_MODULES]
        
     version 1.23.2
        - Added 'importFrom("IRanges", "IRanges")'
        
     version 1.23.1
        - Vignette update
        
     version 1.21.13
        - Adding 'runWF' and 'renderReport' functions
        - Adding new internal fct: '.tryCatchSYS'
        
     version 1.21.12
        - Adding 'plotWF' and 'dataWF' method
        - Adding new internal fct: '.find_long_branch', '.make_plot', '.change_branch' 

     version 1.21.11
        - Adding 'magrittr' ImportsFrom
        
     version 1.21.10
        - Adding new CLASS: "SYSargsList"
        - Adding new Methods: "codeSteps", "projectInfo", "statusWF", "stepsWF", "SYSargs2_steps", "sysargslist", "sysconfig"
        - Adding New functions:[config.param, configWF, initProject, initWF, subsetRmd, SYSprojec]
        - Updating: "SYScreate"
        - Adding new internal functions: ".getPath ", ".getExt ", ".getFileName", ".nest", ".replace", ".sysconfigCheck", ".parse_step"

     version 1.21.9
        - Adding new utilities functions: "evalCode", "tryPath", "tryCL"

     version 1.21.08
        - Implementing deprecated for 'SYSargs2Pipe-class'; it will be replaced for 'SYSargsList'
        
     version 1.21.07
        - Replace name SYSargs2list methods to sysargs2 methods [Motivation: because we are introducing a new class called SYSargsList, to avoid any confusion]
        - BugFix: citation file
        - Updated News file
        
     version 1.21.06
        - Fixed bug: 'runCommandline'
        - Internal functions for runCommandline(): modular and sustainable develp
        - Fixed output_update()
        
     version 1.21.05
        - Fixed bug: 'renderWF': New R version bugs
        
     version 1.21.04
        - Fixed bug: 'runCommandline' modulecmd
        
     version 1.21.03
        - Fixed bug: 'mergeBamByFactor' accepting "FileName" column in any position
        
     version 1.21.02
        - Fixed bug: run_edgeR/run_DESeq2 fct
            - fix for _R_CHECK_LENGTH_1_LOGIC2_ error: " --- failure: the condition has length > 1 ---"
        
     version 1.19.07
        - Added "cwl/*" files:
            - GATK/*
            - bcftools/*
            - varseq/*
        - BugFix: 'runCommandline' and 'writeTargetsout'
        - Updated functions related with VAR-seq workflow
            - variantReport 
            - combineVarReports
            - varSummary
            - filterVars
        - BugFix 'writeTargetsout' function (adding new columns - step)
        
     version 1.19.06
        - Updated vignette
        - Updated functions
        - alignStats
        - symLink2bam
        - subsetWF
        - Updated functions related with Chip-seq workflow
            - countRangeset
            - mergeBamByFactor
            - readComp
            - runDiff
        - Added "cwl/*" files:
            - MACS2/*
            - annotate_peaks/*
            - count_rangesets/*
            - mergeBamByFactor/*
            - rundiff/*

     version 1.19.05
        - **Central vignette for all the Workflows**
        - Updated 'runCommandline':
            - accepts bash command and "$TRINITY"
            - force argument
            - del_sam argument
            - Bugfix "make_bam" and dir=T: "update_output"
        - 'loadWF' function accepts 'targets.txt' OR 'targets.yml' OR 'SYSargs2' object OR NULL  
        - Updated 'writeTargetsout' function (adding new columns)

     version 1.19.04
        - Moved functions from R/AllClasses.R to R/utilities.R
        - Added new function: "olRanges" - R/chipseq.R
        - Added new function: "createWF" + Unexported helper functions: "SYScreate", "write.clt", "write.yml"
        - Added wrapper for loadWorkflow function: Short and consistent name for the function "loadWF"

     version 1.19.03
        - Added "cwl/*" files:
            - hista2/*
            - tophat2/*
            - bowtie2/*
            - bwa/*        
            - rsubread/* 
            - gsnap/* 
            - preprocessReads/* 
            - trim_galore/* 
            - trimmomatic/* 
            - samtools/* 
            - WF_Hisat2_samtools/* 
        - Added "docopt.R/*" folder
        - SYSargs2:
            - Updated *output_update.Rd and *preprocessReads.Rd
            - Removed special cases (`mkdir`)
            - Updated 'subsetWF' function
            - Updated 'output_update' function and help file
            - SYSargs2 accepting many outputs file under one 'cmdlist(WF)'
            - Bugfix in 'pathInstance' fct: removed NULL from the path
            - Bugfix in 'loadWorkflow' fct: it accepts "targets.txt" and "./targets.txt"
        - Updated 'runCommandline' function: 
            - accepting many outputs file under one cmdlist(WF); 
            - handle with BWA specials stderr; 
            - creates an index in cases of .bam files (ex. Tophat2); 
            - automatically create SYSargs2 object with output_update in cases of make_bam=TRUE and/or dir=TRUE; 
            - fix "dir=TRUE"
        - Updated 'writeTargetsout' function (Allowing SYSargs2 object)
        - Updated 'preprocessReads' function and help file
        - Updated all the help files related with SYSargs2
        - Updated vignettes
            
     version 1.19.02
        - Added SYSargs2 to the main vignette
 
     version 1.19.01
        - Fixed bug in runCommandline function - make_bam=TRUE
 
     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