Installation | First Example | Wrap command line tools | Input Parameters | Essential Input parameters | Array Inputs | Output Parameters | Capturing Output | Array Outputs | Running Tools in Docker | Running Tools in Cluster server | Writing Pipeline | Scattering pipeline | Pipeline plot | Web Application | cwlProcess example | cwlProcess to Shiny App | Working with R functions | Resources | RcwlPipelines | Tutorial book | The R recipes and cwl scripts | Tool collections in CWL format | Docker for Bioinformatics tools | SessionInfo
Package: Rcwl 1.29.0
Qiang Hu
Rcwl: An R interface to the Common Workflow Language
The Common Workflow Language (CWL) is an open standard for development of data analysis workflows that is portable and scalable across different tools and working environments. Rcwl provides a simple way to wrap command line tools and build CWL data analysis pipelines programmatically within R. It increases the ease of usage, development, and maintenance of CWL pipelines.
Authors:
Rcwl_1.29.0.tar.gz
Rcwl_1.29.0.zip(r-4.7)Rcwl_1.29.0.zip(r-4.6)Rcwl_1.29.0.zip(r-4.5)
Rcwl_1.29.0.tgz(r-4.6-any)Rcwl_1.29.0.tgz(r-4.5-any)
Rcwl_1.29.0.tar.gz(r-4.7-any)Rcwl_1.29.0.tar.gz(r-4.6-any)
Rcwl_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
Rcwl/json (API)
| # Install 'Rcwl' in R: |
| install.packages('Rcwl', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:Rcwl-1.29.0(bioc 3.24)Rcwl-1.28.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwareworkflowstepimmunooncology
Last updated from:923729b75b. Checks:4 ERROR, 4 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 189 | ||
| linux-devel-x86_64 | NOTE | 1046 | ||
| source / vignettes | OK | 752 | ||
| linux-release-x86_64 | NOTE | 1014 | ||
| macos-release-arm64 | NOTE | 646 | ||
| macos-oldrel-arm64 | NOTE | 624 | ||
| windows-devel | ERROR | 213 | ||
| windows-release | ERROR | 216 | ||
| windows-oldrel | ERROR | 225 | ||
| wasm-release | OK | 166 |
Exports:addMetaargumentsarguments<-baseCommandbaseCommand<-condaPackageCondaToolcwlClasscwlClass<-cwlProcesscwlShinycwlStepcwlStepListcwlVersioncwlVersion<-cwlWorkflowDirentenv_Rcwlextensionsextensions<-hintshints<-InputArrayParamInputParamInputParamListinputsinstall_cwltoolinstall_udockermetameta<-OutputArrayParamOutputParamOutputParamListoutputsplotCWLreadCWLrequireDockerrequireEnvVarrequireInitialWorkDirrequireJSrequireManifestrequirementsrequirements<-requireMultipleInputrequireNetworkrequireResourcerequireRscriptrequireScatterrequireShellCommandrequireShellScriptrequireSoftwarerequireStepInputExpressionrequireSubworkflowrunCWLrunCWLBatchrunCWLBPrunsShellScriptshortstdOutstdOut<-stepInParamstepInParamListstepInputsstepOutputsstepssteps<-writeCWL
Dependencies:backportsbase64encbase64urlbasiliskbatchtoolsBHBiocGenericsBiocParallelbitbit64brewbslibcachemcheckmateclicliprcodetoolscommonmarkcpp11crayondata.tableDiagrammeRdigestdir.expirydplyrevaluatefarverfastmapfilelockfontawesomeformatRfsfutile.loggerfutile.optionsgenericsglueherehighrhmshtmltoolshtmlwidgetshttpuvigraphjquerylibjsonliteknitrlabelinglambda.rlaterlatticelifecyclemagrittrMatrixmemoisemimeotelpillarpkgconfigpngprettyunitsprogresspromisespurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppTOMLreadrreticulaterlangrmarkdownrprojrootrstudioapiS4Vectorssassscalesshinysnowsourcetoolsstringistringrtibbletidyrtidyselecttinytextzdbutf8vctrsviridisLitevisNetworkvroomwithrxfunxtableyaml
Rcwl: An R interface to the Common Workflow Language (CWL)
Last update: 2023-08-03
Started: 2019-02-08
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Rcwl-package | Rcwl,Rcwl-package Rcwl-package Rcwl |
| CWL requirements functions | condaPackage CondaTool cwl-requirements Dirent requireDocker requireEnvVar requireInitialWorkDir requireJS requireManifest requireMultipleInput requireNetwork requireResource requireRscript requireScatter requireShellCommand requireShellScript requireSoftware requireStepInputExpression requireSubworkflow ShellScript |
| Parameters for CWL | cwlProcess |
| cwlProcess methods | $,cwlProcess-method $<-,cwlProcess-method arguments arguments<- baseCommand baseCommand<- cwlClass cwlClass<- cwlProcess-methods cwlVersion cwlVersion<- extensions extensions<- hints hints<- inputs outputs requirements requirements<- short stdOut stdOut<- |
| cwlShiny | cwlShiny |
| cwlStep function | cwlStep |
| cwlWorkflow function | +,cwlWorkflow,cwlStep-method cwlWorkflow steps steps<- |
| cwlWorkflow methods | cwlWorkflow-methods runs |
| Rcwl conda environment | env_Rcwl |
| All classes defined in the package of `Rcwl` and the class constructor functions. | cwlProcess-class cwlStep-class cwlStepList cwlStepList-class cwlWorkflow-class InputArrayParam InputArrayParam-class InputParam InputParam-class InputParamList InputParamList-class OutputArrayParam OutputArrayParam-class OutputParam OutputParam-class OutputParamList OutputParamList-class stepInParam stepInParam-class stepInParamList stepInParamList-class |
| install cwltool | install_cwltool |
| install udocker | install_udocker |
| addMeta Add or change meta information for a cwl recipe. | addMeta meta meta<- |
| plotCWL | plotCWL |
| Read CWL Function to read CWL command or workflow files. | readCWL |
| run cwlProcess | runCWL |
| run CWL with batchtools | runCWLBatch |
| run CWL with BiocParallel | runCWLBP |
| stepInputs | stepInputs |
| stepOutputs | stepOutputs |
| Write CWL | writeCWL |
