changelog version 1.26.3 - Adding createParamFiles, "writeParamFiles", "printParam", "subsetParam", "replaceParam", "renameParam", "appendParam", "updateWF", "SYSargsList" functions - Adding "cmdToCwl", "baseCommand", "sprconfig", "stepsWF", "statusWF", "dependency", "projectWF", "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 1.26.2 - Special case for Rscript version 1.26.1 - 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", "projectWF", "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