View source: R/sysargslist_utilities.R
renderReport | R Documentation |
Render the technical report file to the specified output format using pandoc.
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)
sysargs |
object of class |
fileName |
character string naming a file output. Default is |
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. |
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 |
open_file |
Default is |
It will return an SYSargsList
updated, with the file path location.
Daniela Cassol
See also as SYSargsList-class
.
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)
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