run-PipR-method: run-methods

In MPIIComputationalEpigenetics/muPipeR: muPipeR

run-methods

Description

Run all incomplete analysis steps in the pipeline

Usage

## S4 method for signature 'PipR'
run(object, cmdr = CommandRsystem(logDir = getDir(object,
  "log")), createDirs = TRUE, saveStatus = TRUE, logCommands = FALSE,
  wait = TRUE)

Arguments

object	PipR object
cmdr	CommandR object that will execute all jobs pertaining to each pipeline step.
createDirs	Logical Indicating whether subdirectories for each pipeline step should be created.
saveStatus	Logical indicating whether the PipR object should save itself and the current pipeline graph with annotated steps in the pipeline's status directory.
logCommands	Logical indicating whether the commands that have been used should be written to a log file.
wait	wait for jobs in a step to terminate before continuing to the next one

Details

The method will run all incomplete analysis steps given a CommandR object for executing the jobs pertaining to each step

Value

the modified pipeline object with updated step states.

Author(s)

Fabian Mueller

MPIIComputationalEpigenetics/muPipeR documentation built on Oct. 18, 2022, 2:35 a.m.