renderReport {systemPipeR} | R Documentation

## Render RMarkdown Report

### Description

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

### Usage

    renderReport(sysargs, fileName ="spr_report",
                  rmd_title = "SPR workflow Template - Report",
                  rmd_author = "Author",
                  rmd_date= "Last update: `r format(Sys.time(), '%d %B, %Y')`",
                  type = c("html_document"),
                  desc = "This is a workflow template.",
                  quiet = FALSE, open_file = TRUE)

### Arguments

`sysargs` | object of class `SYSargsList`.
`fileName` | character string naming a file output. Default is `"spr_report.Rmd"`.
`rmd_title` | string, title of the Rmd.
`rmd_author` | string, author(s) of the Rmd, put all authors in a single character string.
`rmd_date` | string, date header of Rmd.
`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"`).
`desc` | string, or character vector of strings, some description text in format Rmarkdown that will be added to the document before the workflow steps start. It can be a single line or multiple lines by providing a character vector, each item is one line.
`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, with the file path location.

### Author(s)

Daniela Cassol

### See Also

See also as `SYSargsList-class`.

### Examples

    sal <- SPRproject(overwrite = TRUE)
    file_path <- system.file("extdata", "spr_simple_wf.Rmd", package = "systemPipeR")
    sal <- importWF(sal, file_path = file_path, verbose = FALSE)
    targetspath <- system.file("extdata/cwl/example/targets_example.txt", package = "systemPipeR")
    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_"))
    sal <- renderReport(sal, open_file = FALSE)

[Package systemPipeR version 2.0.8 Index]