Write updated targets out to file from SYSargsList

Convenience write function for generating targets files containing the paths to files generated by input processes. These processes can be commandline- or R-based software. Typically, the paths to the inputs are stored in the targets infile targetsWF(sysargs) for SYSargsList objects. Note: by default the function cannot overwrite any existing files. If a file exists then the user has to explicitly remove it or set overwrite=TRUE.

writeTargets(sysargs, step, file = "default", silent = FALSE, overwrite = FALSE)

Arguments

sysargs: Object of class SYSargsList.
step: character with the step name. To check all the names, please use stepName(sysargs).
file: Name and path of the output file. If set to "default" then the name of the output file will have the pattern 'targets_<stepName>.txt'.
silent: If set to TRUE, all messages returned by the function will be suppressed.
overwrite: If set to TRUE, existing files of same name will be overwritten.

Value

Writes tabular targes files containing the header/comment lines from

stepsWF(sysargs)[[step]][["targetsheader"]] and the columns from targetsWF(sysargs)[[step]].

Author

Daniela Cassol

Examples

## Construct SYSargsList object from Rmd file
sal <- SPRproject(overwrite=TRUE)
#> Recreating directory '/home/runner/work/systemPipeR/systemPipeR/docs/reference/.SPRproject'
#> Creating file '/home/runner/work/systemPipeR/systemPipeR/docs/reference/.SPRproject/SYSargsList.yml'
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")
writeTargets(sal, "echo")
#> 	 Written content of 'targetsout(x)' to file: targets_echo.txt