renderReport: Render RMarkdown Report

In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description

Render the input file to the specified output format using pandoc.

Usage

renderReport(sysargslist, type = c("html_document"))

Arguments

sysargslist	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").

Value

It will return an SYSargsList updated.

Author(s)

Daniela Cassol and Thomas Girke

See Also

See also as SYSargsList-class.

Examples

## Not run: 
## Construct SYSargsList object from Rmd file
library(systemPipeRdata)
script <- system.file("extdata/workflows/rnaseq", "systemPipeRNAseq.Rmd", package="systemPipeRdata")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
dir_path <- tempdir()
SYSconfig <- initProject(projPath=dir_path, targets=targets, script=script, overwrite = TRUE)
sysargslist <- initWF(sysconfig ="SYSconfig.yml")
sysargslist <- configWF(x=sysargslist, input_steps = "1:3")
sysargslist <- runWF(sysargslist = sysargslist, steps = "ALL")
renderReport(x=sysargslist)

## End(Not run)

systemPipeR documentation built on Jan. 26, 2021, 2 a.m.