Package: pipeFrame 1.21.0
Zheng Wei
pipeFrame: Pipeline framework for bioinformatics in R
pipeFrame is an R package for building a componentized bioinformatics pipeline. Each step in this pipeline is wrapped in the framework, so the connection among steps is created seamlessly and automatically. Users could focus more on fine-tuning arguments rather than spending a lot of time on transforming file format, passing task outputs to task inputs or installing the dependencies. Componentized step elements can be customized into other new pipelines flexibly as well. This pipeline can be split into several important functional steps, so it is much easier for users to understand the complex arguments from each step rather than parameter combination from the whole pipeline. At the same time, componentized pipeline can restart at the breakpoint and avoid rerunning the whole pipeline, which may save a lot of time for users on pipeline tuning or such issues as power off or process other interrupts.
Authors:
pipeFrame_1.21.0.tar.gz
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pipeFrame.pdf |pipeFrame.html✨
pipeFrame/json (API)
NEWS
| # Install 'pipeFrame' in R: |
| install.packages('pipeFrame', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/wzthu/pipeframe/issues
On BioConductor:pipeFrame-1.21.0(bioc 3.20)pipeFrame-1.20.0(bioc 3.19)
Last updated 2 months agofrom:e97ea2e82c
Exports:addEdgesaddFileSuffixargvcheckAllPathcheckAndInstallBSgenomecheckAndInstallGenomeFacheckAndInstallOrgDbcheckAndInstallTxDbcheckFileCreatablecheckFileExistcheckPathExistcheckRequireParamclearStepCacheconfigRegNamegenReportgetAttachedStepgetAutoPathgetBasenamePrefixgetGenomegetJobDirgetJobNamegetNextStepsgetObjsInPipegetParamgetParamItemsgetParamMD5PathgetPathPrefixgetPipeNamegetPrevStepsgetRefgetRefDirgetRefFilesgetRefRcgetStepWorkDirgetThreadsgetTmpDirgetValidGenomeignoreCheckinitinitPipeFrameinputinput<-isReadyloadConfigloadStepoutputoutput<-paramparam<-pipeNameprintMapprocessingpropertyproperty<-regAttachedStepreportreport<-runWithFinishChecksaveConfigsetGenomesetJobNamesetPipeNamesetRefDirsetThreadssetTmpDirStepstepIDstepNamestepTypewriteLog
Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopsBSgenomebslibcachemclicodetoolscpp11crayoncurlDelayedArraydigestevaluatefastmapfontawesomeformatRfsfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgluehighrhtmltoolshtmlwidgetshttrIRangesjquerylibjsonliteknitrlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslR6rappdirsRCurlrestfulrRhtslibrjsonrlangrmarkdownRsamtoolsrtracklayerS4ArraysS4VectorssasssnowSparseArraySummarizedExperimentsystinytexUCSC.utilsvisNetworkxfunXMLXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Obtain all of objects in the specific pipeline | getObjsInPipe |
| Step graph management | addEdges getAttachedStep getNextSteps getPrevSteps graphMng printMap regAttachedStep |
| ignore checking input and output file (for developer) | ignoreCheck |
| initialize the pipeFrame package | initPipeFrame |
| load configure from file | configRegName loadConfig saveConfig |
| load step object from rds file | loadStep |
| Install dependent data or software with finishing check | checkAndInstallBSgenome checkAndInstallGenomeFa checkAndInstallOrgDb checkAndInstallTxDb runWithFinishCheck |
| Configure genome for all steps | getGenome getValidGenome setGenome |
| Configure the job name for following steps. | getJobDir getJobName setJobName |
| Configure the pipe name for following steps. | getPipeName setPipeName |
| Set the reference directory | getRef getRefDir getRefFiles getRefRc setRefDir |
| Configure the maximum number of threads | getThreads setThreads |
| Configure the directory for intermediate results of all steps | getTmpDir setTmpDir |
| Methods for Step objects | $ $,Step-method $<- $<-,Step-method argv argv,Step-method checkAllPath checkAllPath,Step-method checkRequireParam checkRequireParam,Step-method clearStepCache clearStepCache,Step-method genReport getAutoPath getAutoPath,Step-method getParam getParam,Step-method getParamItems getParamItems,Step-method getParamMD5Path getParamMD5Path,Step-method getStepWorkDir getStepWorkDir,Step-method init init,Step-method input input,Step-method input<- input<-,Step-method isReady isReady,Step-method output output,Step-method output<- output<-,Step-method param param,Step-method param<- param<-,Step-method pipeName pipeName,Step-method processing property property,Step-method property<- property<-,Step-method report report,Step-method report<- report<-,Step-method Step Step-class stepID stepID,Step-method stepName stepName,Step-method stepType stepType,Step-method writeLog writeLog,Step-method |
| Functions for directory operations | addFileSuffix checkFileCreatable checkFileExist checkPathExist getBasenamePrefix getPathPrefix Utils |
