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

See Also

See also as SYSargsList-class.

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]