Introduction | Design overview | CL interface (CLI) | Workflow templates | Other functionalities | Quick start | Installation | Five minute tutorial | Directory structure | The targets file | Single-end (SE) data | Paired-end (PE) data | Sample comparisons | Detailed tutorial | Initialization | Constructing workflows | Stepwise construction | Step 1: R step | Step 2: CL step | Step 3: CL with input from previous step | Step 4: R with input from previous step | Load workflow from R or Rmd scripts | Define workflow steps in R Markdowns | Running workflows | Overview | Module system | Parallel evaluation | Visualize workflows | Report generation | Scientific reports | Technical report | Converting workflows to Bash and Rmd | R Markdown script | Bash script | Restarting and resetting workflows | Additional utilities | Accessor methods | General information | Slot data | CL and R code | R environment | Subsetting workflows | Replacement methods | Changing parameters | Changes to R steps | Replacing workflow steps | CWL specifications | CWL CommandLineTool | CWL Workflow | CWL input values | Mappings among cwl, yml and targets | Assembly of CL calls from three files | Auto-creation of CWL files | Expected CL syntax | createParam Function | Example with targets file | Utilities for CWL files | Printing components | Subsetting the CL strings | Replacing existing arguments | Adding new arguments | Editing output parameters | Workflow step classes | SYSargs2 class | LineWise Class | Supplemental Material | Examples of CL software | Data analysis functionalities | Project initialization | Read Preprocessing | Preprocessing with preprocessReads function | Preprocessing with TrimGalore! | Preprocessing with Trimmomatic | FASTQ quality report | NGS Alignment software | HISAT2 | Tophat2 | Bowtie2 | BWA-MEM | Rsubread | gsnap | BAM file viewing in IGV | Read counting for mRNA profiling experiments | Read and alignment stats | Read counting for miRNA profiling experiments | Correlation analysis of samples | DEG analysis with edgeR | DEG analysis with DESeq2 | Venn Diagrams | GO term enrichment analysis of DEGs | Obtain gene-to-GO mappings | Batch GO term enrichment analysis | Plot batch GO term results | Clustering and heat maps | Version information | Funding | References
Package: systemPipeR 2.19.0
Thomas Girke
systemPipeR: systemPipeR: A Multipurpose Workflow Management System for Reproducible Data Analysis
systemPipeR is a workflow management environment for reproducible data analysis that integrates R with command-line software. It enables researchers to design, execute, and report complex workflows on local machines and HPC systems. The framework combines R-based analysis with external tools through a Common Workflow Language (CWL) interface, manages workflow dependencies and restart capabilities, and automatically generates reproducible scientific analysis reports. The companion package systemPipeRdata provides ready-to-use workflow templates that simplify workflow setup and customization. Alternatively, workflow templates can be loaded from dedicated GitHub repositories.
Authors:
systemPipeR_2.19.0.tar.gz
systemPipeR_2.19.0.zip(r-4.7)systemPipeR_2.19.0.zip(r-4.6)systemPipeR_2.19.0.zip(r-4.5)
systemPipeR_2.19.0.tgz(r-4.6-any)systemPipeR_2.19.0.tgz(r-4.5-any)
systemPipeR_2.19.0.tar.gz(r-4.7-any)systemPipeR_2.19.0.tar.gz(r-4.6-any)
systemPipeR_2.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
systemPipeR/json (API)
| # Install 'systemPipeR' in R: |
| install.packages('systemPipeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tgirke/systempiper/issues
On BioConductor:systemPipeR-2.19.0(bioc 3.24)systemPipeR-2.18.0(bioc 3.23)
geneticsinfrastructuredataimportsequencingrnaseqriboseqchipseqmethylseqsnpgeneexpressioncoveragegenesetenrichmentalignmentqualitycontrolimmunooncologyreportwritingworkflowstepworkflowmanagement
Last updated from:d92e8e37d2. Checks:8 ERROR, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 279 | ||
| linux-devel-x86_64 | ERROR | 513 | ||
| source / vignettes | OK | 362 | ||
| linux-release-x86_64 | ERROR | 631 | ||
| macos-release-arm64 | ERROR | 481 | ||
| macos-oldrel-arm64 | ERROR | 327 | ||
| windows-devel | ERROR | 505 | ||
| windows-release | ERROR | 538 | ||
| windows-oldrel | ERROR | 514 | ||
| wasm-release | OK | 242 |
Exports:addResourcesalignStatsappendCodeLine<-appendParamappendParam2appendStep<-as.listbaseCommandcatlistcatmapcheck.outfilescheck.outputcltclusterRuncmdlistcmdToCwlcmdToCwl<-codeChunkStartcodeLinecombineVarReportscomplexitylevelsconfig.paramconfigWFcopyEnvircorescountRangesetcreateParamcreateParamFilescwlFilesUpdatedependencydependency<-evalCodefeatureCoveragefeaturetypeCountsfilesfilterDEGsfilterVarsgenFeaturesgetColumngoBarplotGOCluster_ReportGOHyperGAllGOHyperGAll_SimplifyGOHyperGAll_SubsetidconvimportWFinfile1infile2inputinputvarsintersectlistintersectmatrixlinewiseLineWiselistCmdModuleslistCmdToolsloadWFloadWorkflowmakeCATdbmergeBamByFactormodulemoduleAvailmoduleClearmoduleInitmodulelistmoduleloadmodulesmoduleUnloadolBarplotolRangesotheroutfile1outfilesoutpathsoutputoutput_updateoverLapperplotfeatureCoverageplotfeaturetypeCountsplotWFplotwfOutputpredORFpreprocessReadsprintParamprintParam2projectInforeadCompreferenceremoveParam2renameParamrenameParam2renameStep<-renderLogsrenderPlotwfrenderReportrenderWFreplaceCodeLine<-replaceParamreplaceParam2replaceStep<-resultsreturnRPKMrmdPathrun_DESeq2run_edgeRrunCommandlinerunDiffrunInforunWFsal2bashsal2rmdSampleNamescaleRangesSESE<-seeFastqseeFastqPlotsetlistshowshowDFsoftwareSPRprojectstatusstatusWFstepNamestepsWFsubsetsubsetParamsubsetWFsymLink2bamsysargssysargs2sysargslistSYSargsListsystemArgstargetstargets.as.dftargets.as.listtargetsheadertargetsintargetsouttargetsWFtrimbatchtryCLtryCMDtryPathupdateColumn<-updateWFvariantReportvarSummaryvennlistvennPlotviewEnvirwfwrite_SYSargsListwriteParamFileswriteTargetswriteTargetsoutwriteTargetsRefyamlinputyamlinput<-
Dependencies:abindbase64encBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbslibcachemcigarilloclicodetoolscpp11crayonDelayedArraydeldirdigestevaluatefarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehighrhtmltoolshtmlwidgetshwriterinterpIRangesisobandjpegjquerylibjsonliteknitrlabelinglambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimepngpwalignR6rappdirsRColorBrewerRcppRcppEigenRhtslibrlangrmarkdownRsamtoolsS4ArraysS4VectorsS7sassscalesSeqinfoShortReadsnowSparseArraystringistringrSummarizedExperimenttinytexvctrsviridisLitewithrxfunXVectoryaml
systemPipeR: Workflow Environment for Data Analysis and Report Generation
Last update: 2026-03-06
Started: 2015-07-27
systemPipeR: Workflow Templates
Redirect notification | Funding
Last update: 2024-07-28
Started: 2019-10-15
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| systemPipeR package for Workflow Environment | systemPipeR-package |
| Extension accessor methods for SummarizedExperiment object | addAssay addAssay,SummarizedExperiment-method addAssay-methods addMetadata addMetadata,SummarizedExperiment-method addMetadata-methods |
| Alignment statistics | alignStats |
| Class '"catDB"' | catDB-class catlist,catDB-method catmap,catDB-method coerce,list,catDB-method idconv,catDB-method names,catDB-method show,catDB-method |
| catDB accessor methods | catlist catlist-methods catmap catmap-methods idconv idconv-methods |
| Checking if the outfiles files exist | check.outfiles check.output |
| Submit command-line tools to cluster | clusterRun |
| Adding param file | config.param |
| Workflow Steps Selection | configWF |
| Read counting for several range sets | countRangeset |
| createParam | createParam createParamFiles writeParamFiles |
| Update CWL description files | cwlFilesUpdate |
| Class '"EnvModules"' | $,EnvModules-method available_modules,EnvModules-method coerce,EnvModules,list-method coerce,list,EnvModules-method default_modules,EnvModules-method EnvModules,EnvModules-method EnvModules-class loaded_modules,EnvModules-method modulecmd,EnvModules-method names,EnvModules-method show,EnvModules-method [,EnvModules,ANY,ANY,ANY-method [[,EnvModules,ANY,ANY-method [[,EnvModules,ANY,missing-method [[<-,EnvModules,ANY,ANY,ANY-method [[<-,EnvModules,ANY,ANY-method [[<-,EnvModules-method |
| Toggles option 'eval' on the RMarkdown files | evalCode |
| Genome read coverage by transcript models | featureCoverage |
| Plot read distribution across genomic features | featuretypeCounts |
| Filter and plot DEG results | filterDEGs |
| Filter VCF files | filterVars |
| Generate feature ranges from TxDb | genFeatures |
| GO term enrichment analysis for large numbers of gene sets | goBarplot GOCluster_Report GOHyperGAll GOHyperGAll_Simplify GOHyperGAll_Subset makeCATdb |
| Import R Markdown file as workflow | importWF |
| Class '"INTERSECTset"' | as.list,INTERSECTset-method coerce,list,INTERSECTset-method complexitylevels,INTERSECTset-method intersectlist,INTERSECTset-method intersectmatrix,INTERSECTset-method INTERSECTset-class length,INTERSECTset-method names,INTERSECTset-method setlist,INTERSECTset-method show,INTERSECTset-method |
| Class '"LineWise"' | $,LineWise-method appendCodeLine,LineWise-method appendCodeLine<-,LineWise-method codeChunkStart codeChunkStart,LineWise-method codeLine,LineWise-method coerce,LineWise,list-method coerce,list,LineWise-method dependency,LineWise-method files,LineWise-method length,LineWise-method LineWise linewise linewise,LineWise-method LineWise-class names,LineWise-method replaceCodeLine,LineWise-method replaceCodeLine<-,LineWise-method rmdPath rmdPath,LineWise-method runInfo,LineWise-method show,LineWise-method status,LineWise-method stepName,LineWise-method [,LineWise,ANY,ANY,ANY-method [[,LineWise,ANY,missing-method [[<-,LineWise,ANY,ANY,ANY-method [[<-,LineWise,ANY,ANY-method |
| List/check the existence of command-line tools of a workflow | listCmdModules listCmdTools |
| Constructs SYSargs2 object from CWL param and targets files | loadWF loadWorkflow renderWF updateWF |
| Merge BAM files based on factor | mergeBamByFactor |
| Interface to allow full use of the Environment Modules system for Unix | module moduleAvail moduleClear moduleInit modulelist moduleload moduleUnload |
| Bar plot for intersect sets | olBarplot |
| Identify Range Overlaps for IRanges and GRanges Object | olRanges |
| Updates the output files paths in the 'SYSargs2' object | output_update |
| Set Intersect and Venn Diagram Functions | complexitylevels complexitylevels-methods intersectlist intersectlist-methods intersectmatrix intersectmatrix-methods overLapper setlist setlist-methods vennlist vennlist-methods |
| Plot feature coverage results | plotfeatureCoverage |
| Plot read distribution across genomic features | plotfeaturetypeCounts |
| Visualize SPR workflow and status | plotWF plotwfOutput renderPlotwf |
| Predict ORFs | predORF |
| Run custom read preprocessing functions | preprocessReads |
| Accessories function to modify the Command-line Version 1 | appendParam printParam renameParam replaceParam subsetParam |
| Accessories function to modify the Command-line Version 2 | appendParam2 printParam2 removeParam2 renameParam2 replaceParam2 |
| Import sample comparisons from targets file | readComp |
| Render RMarkdown Logs Report | renderLogs |
| Render RMarkdown Report | renderReport |
| RPKM Normalization | returnRPKM |
| Runs DESeq2 | run_DESeq2 |
| Runs edgeR | run_edgeR |
| Execute SYSargs and SYSargs2 | runCommandline |
| Differential abundance analysis for many range sets | runDiff |
| Execute SYSargsList | runWF |
| Translate SYSargsList back to a bash workflow | sal2bash |
| Translate SYSargsList back to a workflow template Rmarkdown file | sal2rmd |
| Scale spliced ranges to genome coordinates | scaleRanges |
| Quality reports for FASTQ files | seeFastq seeFastqPlot |
| Create an HTML table using DT package with fixed columns | showDF |
| Workflow Project Initiation | SPRproject |
| Subsetting SYSargs2 class slots | subsetWF |
| Symbolic links for IGV | symLink2bam |
| SYSargs accessor methods | cores cores-methods infile1 infile1-methods infile2 infile2-methods modules-methods other other-methods outfile1 outfile1-methods outpaths outpaths-methods reference reference-methods results results-methods SampleName-methods software software-methods sysargs sysargs-methods targetsheader-methods targetsin targetsin-methods targetsout targetsout-methods |
| Class '"SYSargs"' | coerce,list,SYSargs-method cores,SYSargs-method infile1,SYSargs-method infile2,SYSargs-method length,SYSargs-method modules,SYSargs-method names,SYSargs-method other,SYSargs-method outfile1,SYSargs-method outpaths,SYSargs-method reference,SYSargs-method results,SYSargs-method SampleName,SYSargs-method show,SYSargs-method software,SYSargs-method sysargs,SYSargs-method SYSargs-class targetsheader,SYSargs-method targetsin,SYSargs-method targetsout,SYSargs-method [,SYSargs,ANY,ANY,ANY-method |
| Class '"SYSargs2"' | $,SYSargs2-method baseCommand,SYSargs2-method clt clt,SYSargs2-method cmdlist,SYSargs2-method cmdToCwl cmdToCwl,SYSargs2-method cmdToCwl<- cmdToCwl<-,SYSargs2-method coerce,list,SYSargs2-method coerce,SYSargs2,list-method files files,SYSargs2-method infile1,SYSargs2-method infile2,SYSargs2-method input input,SYSargs2-method inputvars inputvars,SYSargs2-method internal_outfiles internal_outfiles,SYSargs2-method length,SYSargs2-method modules modules,SYSargs2-method names,SYSargs2-method output output,SYSargs2-method SampleName,SYSargs2-method show,SYSargs2-method status status,SYSargs2-method sysargs2 sysargs2,SYSargs2-method SYSargs2-class targets targets,SYSargs2-method targetsheader,SYSargs2-method wf wf,SYSargs2-method yamlinput,SYSargs2-method yamlinput<-,SYSargs2,ANY,ANY-method yamlinput<-,SYSargs2-method [,SYSargs2,ANY,ANY,ANY-method [[,SYSargs2,ANY,missing-method [[<-,SYSargs2,ANY,ANY,ANY-method [[<-,SYSargs2,ANY,ANY-method |
| SYSargsList Constructor | SYSargsList |
| Class '"SYSargsList"' | $,SYSargsList-method addResources addResources,SYSargsList-method appendCodeLine<- appendCodeLine<-,SYSargsList-method appendStep<- appendStep<-,SYSargsList-method baseCommand baseCommand,SYSargsList-method cmdlist cmdlist,SYSargsList-method codeLine codeLine,SYSargsList-method coerce,list,SYSargsList-method coerce,SYSargsList,list-method copyEnvir copyEnvir,SYSargsList-method dependency dependency,SYSargsList-method dependency<- dependency<-,SYSargsList-method getColumn getColumn,SYSargsList-method length,SYSargsList-method names,SYSargsList-method outfiles outfiles,SYSargsList-method projectInfo projectInfo,SYSargsList-method renameStep<- renameStep<-,SYSargsList-method replaceCodeLine<- replaceCodeLine<-,SYSargsList-method replaceStep<- replaceStep<-,SYSargsList-method runInfo runInfo,SYSargsList-method SampleName SampleName,SYSargsList-method SE SE,SYSargsList-method SE<- SE<-,SYSargsList-method show,SYSargsList-method statusWF statusWF,SYSargsList-method stepName stepName,SYSargsList-method stepsWF stepsWF,SYSargsList-method subset subset,SYSargsList-method sysargslist sysargslist,SYSargsList-method SYSargsList-class targetsheader targetsheader,SYSargsList-method targetsWF targetsWF,SYSargsList-method targets_connection targets_connection,SYSargsList-method updateColumn<- updateColumn<-,SYSargsList-method viewEnvir viewEnvir,SYSargsList-method yamlinput yamlinput,SYSargsList-method yamlinput<- yamlinput<-,SYSargsList-method [,SYSargsList,ANY,ANY,ANY-method [[,SYSargsList,ANY,missing-method [[<-,SYSargsList,ANY,ANY,ANY-method [[<-,SYSargsList,ANY,ANY-method |
| Constructs SYSargs object from param and targets files | systemArgs |
| Convert targets to list or data.frame | targets.as.df targets.as.list |
| Genome read coverage by transcript models | trimbatch |
| Collect information about the third-party software | tryCL tryCMD |
| Validation of the files or directories | tryPath |
| Generate Variant Report | combineVarReports variantReport varSummary |
| Plot 2-5 way Venn diagrams | vennPlot |
| Class '"VENNset"' | as.list,VENNset-method coerce,list,VENNset-method complexitylevels,VENNset-method intersectmatrix,VENNset-method length,VENNset-method names,VENNset-method setlist,VENNset-method show,VENNset-method vennlist,VENNset-method VENNset-class |
| Writeout SYSargsList object | write_SYSargsList |
| Write updated targets out to file from 'SYSargsList' | writeTargets |
| Write updated targets out to file | writeTargetsout |
| Generate targets file with reference | writeTargetsRef |
