renderReport: Render RMarkdown Logs Report

In tgirke/systemPipeR: systemPipeR: NGS workflow and report generation environment

Description

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

Usage

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

## 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.