runWF: Execute SYSargsList
In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description Usage Arguments Value Author(s) See Also Examples

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

1	runWF(sysargslist, steps = "ALL")

sysargslist

object of class SYSargsList.

steps

a character vector of all steps desires to preserve on the output file. Default is "ALL". It can be used the symbol ":" to select many steps in sequence, for example, input_steps=1:5.2, from step 1 to step 5.2. The symbol "." represents the substeps and symbol "," is used to separate selections. Jump from a major step to sub-step is supported, but if a major step is selected, all sub-steps of this major step will be selected. Repeatedly selected steps will only result in a unique step. It is recommended to put major steps in input_steps, like 1:4, 6:8, 10; and unwanted sub-steps in exclude_step, like 1.1, 3.1.1-3.1.3, 6.5. Reverse selecting is supported e.g. 10:1.

It will return an SYSargsList updated.

Daniela Cassol and Thomas Girke

See also as SYSargsList-class.

## 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(sysconfig ="SYSconfig.yml")
sysargslist <- configWF(x=sysargslist, input_steps = "1:3")
sysargslist <- runWF(sysargslist = sysargslist, steps = "ALL")
sysargslist <- runWF(sysargslist = sysargslist, steps = "1:2")

## End(Not run)