This function allows the user to control of which step of the workflow will be run and the generation of the new RMarkdown.

configWF(x, input_steps = "ALL", exclude_steps = NULL, silent = FALSE, ...)



object of class SYSargsList.


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/excluded, all sub-steps of this major step will be selected/excluded. 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.


a character vector of all steps desires to remove on the output file.


if set to TRUE, all messages returned by the function will be suppressed.


Additional arguments to pass on to configWF().


Daniela Cassol


if (FALSE) {
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
script <- system.file("extdata/workflows/rnaseq", "systemPipeRNAseq.Rmd", package="systemPipeRdata")
SYSconfig <- initProject(projPath="./", targets=targets, script=script, overwrite=TRUE, silent=TRUE)

sysargslist <- configWF(x=sysargslist)