changelog 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