renderLogs {systemPipeR} | R Documentation

## Render RMarkdown Logs Report

### Description

Render the logs report file to the specified output format using pandoc.

### Usage

    renderLogs(sysargs, type = c("html_document", "pdf_document"),
                fileName = "default", quiet = FALSE,
                open_file = TRUE)

### Arguments

`sysargs` | object of class `SYSargsList`.
`type` | The R Markdown output format to convert to. The option can be the name of a format (e.g. `"pdf_document"` or `"html_document"`).
`fileName` | character string naming a file output. Default is `"logs_<date>.Rmd"`.
`quiet` | If set to `TRUE`, all messages returned by the function will be suppressed.
`open_file` | Default is `TRUE`.

### Value

It will return an `SYSargsList` updated.

### 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 <- runWF(sal)
    sal <- renderLogs(sal, open_file = FALSE)

[Package systemPipeR version 2.0.8 Index]