Description

Render an rmarkdown notebook. Supports parametrization.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

notebook (file)

Rmarkdown file

*.{Rmd}

parameters (map)

Groovy map with notebook parameters which will be passed to
rmarkdown to generate parametrized reports.

input_files (file)

One or multiple files serving as input data for the notebook.

*

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

report (file)

HTML report generated from Rmarkdown

*.html

session_info (file)

dump of R SessionInfo

*.log

versions (file)

File containing software versions

versions.yml
included in
differentialabundance
author
Github user grst
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

rmarkdown
GPL-3

Dynamic Documents for R

rmarkdown.rstudio.com rmarkdown.rstudio.com/lesson-1 https://github.com/rstudio/rmarkdown