runWF {systemPipeR} | R Documentation |
Function to execute all the code list specified in SYSargsList object.
runWF(sysargs, steps = NULL, targets = NULL, force = FALSE, saveEnv = TRUE, run_step = "ALL", ignore.dep = FALSE, warning.stop = FALSE, error.stop = TRUE, silent = FALSE, ...)
sysargs |
object of class |
steps |
character or numeric. Step name or index. If |
targets |
This option allows selecting which targets file and, by consequence which
command line will be executed for each |
force |
Internally, the option checks if the expected |
saveEnv |
If set to |
run_step |
character. If the step has "mandatory" or "optional" flag for the execution.
When |
ignore.dep |
logical. This option allow to igonore the dependency tree, when |
warning.stop |
If set to |
error.stop |
If set to |
silent |
If set to |
... |
Additional arguments to pass on from |
It will return an SYSargsList
updated.
Daniela Cassol and Thomas Girke
See also as SYSargsList-class
.
## Construct SYSargsList object from Rmd file sal <- SPRproject(overwrite=TRUE) targetspath <- system.file("extdata/cwl/example/targets_example.txt", package="systemPipeR") ## Constructor and `appendStep<-` appendStep(sal) <- SYSargsList(step_name = "echo", targets=targetspath, dir=TRUE, wf_file="example/workflow_example.cwl", input_file="example/example.yml", dir_path = system.file("extdata/cwl", package="systemPipeR"), inputvars = c(Message = "_STRING_", SampleName = "_SAMPLE_")) appendStep(sal) <- LineWise(code = { hello <- lapply(getColumn(sal, step=1, 'outfiles'), function(x) yaml::read_yaml(x)) }, step_name = "R_read", dependency = "echo") ## Not run: sal <- runWF(sal) ## End(Not run)