runWF {systemPipeR} | R Documentation

## Execute SYSargsList

### Description

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

### Usage

    runWF(sysargs, steps = NULL, targets = NULL,
                      force = FALSE, saveEnv = TRUE,
                      run_step = "ALL", ignore.dep = FALSE,
                      warning.stop = FALSE, error.stop = TRUE, silent = FALSE, ...)

### Arguments

`sysargs` | object of class `SYSargsList`.
`steps` | character or numeric. Step name or index. If `NULL`, all the steps will be executed.
`targets` | This option allows selecting which targets file and, by consequence which command line will be executed for each `SYSargs2` class step. Default is `NULL`, in which all command lines will be executed.
`force` | Internally, the option checks if the expected `output` files exist, and it skips the command lines when the respective files exist. If the argument `force` is set to `TRUE`, the command line will be executed and the files overwrite. Default is `force=FALSE`.
`saveEnv` | If set to `TRUE`, the environment will be saved to an RDS file. To check the RDS file location, please use `projectInfo(sysargs)[["envir"]]`.
`run_step` | character. If the step has "mandatory" or "optional" flag for the execution. When `ALL`, all the steps will be executed.
`ignore.dep` | logical. This option allow to igonore the dependency tree, when `TRUE`.
`warning.stop` | If set to `TRUE`, the process will be interrupted when a warning is detected.
`error.stop` | If set to `TRUE`, the process will be interrupted when a error is detected.
`silent` | If set to `TRUE`, all messages returned by the function will be suppressed.
`...` | Additional arguments to pass on from `runCommandline()`.

### Value

It will return an `SYSargsList` updated.

### Author(s)

Daniela Cassol and Thomas Girke

### See Also

See also as `SYSargsList-class`.

### Examples

    ## 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)

[Package systemPipeR version 2.0.8 Index]