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]