Render RMarkdown Logs Report

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

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

Daniela Cassol

See also

See also as SYSargsList-class.

Examples

## Construct SYSargsList object from Rmd file
sal <- SPRproject(overwrite=TRUE)
#> Recreating directory '/home/runner/work/systemPipeR/systemPipeR/docs/reference/.SPRproject'
#> Creating file '/home/runner/work/systemPipeR/systemPipeR/docs/reference/.SPRproject/SYSargsList.yml'
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)
#> Running Step:  echo 
#> Running Session: Management 
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |======================================================================| 100%
#> ---- Summary ---- 
#>    Targets Total_Files Existing_Files Missing_Files    echo
#> M1      M1           1              1             0 Success
#> M2      M2           1              1             0 Success
#> M3      M3           1              1             0 Success
#> 
#> Step Status:  Success 
#> Running Step:  R_read 
#> Running Session: Management 
#> 
  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
#> Step Status:  Success 
#> 
sal <- renderLogs(sal, open_file = FALSE)
#> 
#> Attaching package: ‘BiocStyle’
#> The following object is masked from ‘package:systemPipeR’:
#> 
#>     output
#> Written content of 'Report' to file: 
#>  logs_May112023_0153.html