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)



Object of class SYSargsList.


character with the step name. To check all the names, please use stepName(sysargs).


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'.


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


If set to TRUE, existing files of same name will be overwritten.


Writes tabular targes files containing the header/comment lines from

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


Daniela Cassol


## 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