R: Execute SYSargsList

runWF {systemPipeR}

R Documentation

Execute SYSargsList

Description

Function to execute all the code list specified in SYSargsList object.

Usage

runWF(args, warning.stop=FALSE, error.stop=TRUE, silent=FALSE)

Arguments

`args`	object of class `SYSargsList`.
`warning.stop`	If set to `TRUE`, the process will be interrupted when a warning is detected.
`error.stop`	If set to `TRUE`, the process will be interrupted when a error is detected.
`silent`	If set to `TRUE`, all messages returned by the function will be suppressed.

Value

It will return an SYSargsList updated.

Author(s)

Daniela Cassol and Thomas Girke

Examples

## Not run: 
## Construct SYSargsList object from Rmd file
library(systemPipeRdata)
script <- system.file("extdata/workflows/rnaseq", "systemPipeRNAseq.Rmd", package="systemPipeRdata")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
dir_path <- tempdir()
SYSconfig <- initProject(projPath=dir_path, targets=targets, script=script, overwrite = TRUE)
sysargslist <- initWF(sprconfig ="SPRconfig.yml")
sysargslist <- configWF(x=sysargslist, input_steps = "1:3")
sal <- runWF(args = sysargslist)

## End(Not run)

[Package systemPipeR version 1.26.3 Index]