renderReport: Render RMarkdown Logs Report

Description Usage Arguments Value Author(s) See Also Examples

View source: R/sysargslist_utilities.R

Description

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

Usage

1
renderLogs(sysargs, type = "html_document", fileName = "default", silent = FALSE)

Arguments

sysargs

object of class SYSargsList.

type

The R Markdown output format to convert to. Default is "ALL".The option can be the name of a format (e.g. "pdf_document" or "html_document").

fileName

haracter string naming a file output. Default is "logs_<date>.Rmd".

silent

If set to TRUE, all messages returned by the function will be suppressed.

Value

It will return an SYSargsList updated.

Author(s)

Daniela Cassol and Thomas Girke

See Also

See also as SYSargsList-class.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
## 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")
## Not run: 
sal <- runWF(sal)
sal <- renderLogs(sal)

## End(Not run)

tgirke/systemPipeR documentation built on July 20, 2021, 10:45 p.m.