write_SYSargsList {systemPipeR} | R Documentation

## Writeout SYSargsList object

### Description

Function to writeout `SYSargsList` workflow control environment (S4 object) object.

### Usage

    write_SYSargsList(sysargs, sys.file=".SPRproject/SYSargsList.yml", silent=TRUE)

### Arguments

`sysargs` | object of class `SYSargsList`.
`sys.file` | name and path of the SYSargsList file which will store all the project configuration information. Default is `.SPRproject/SYSargsList.yml`.
`silent` | if set to TRUE, all messages returned by the function will be suppressed.

### Value

`write_SYSargsList` will return a `sys.file` path.

### Author(s)

Daniela Cassol

### 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")

    sal <- write_SYSargsList(sal)
    sal

[Package systemPipeR version 2.0.8 Index]