renderLogs: Render RMarkdown Logs Report

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

Render RMarkdown Logs Report

Description

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

Usage

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(s)

Daniela Cassol

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")
sal <- runWF(sal)
sal <- renderLogs(sal, open_file = FALSE)

tgirke/systemPipeR documentation built on Aug. 30, 2022, 10 p.m.