Nextflow Registry | nf-core/rmarkdownnotebook@0.0.0-0c7146d

nf-core/rmarkdownnotebook @ 0.0.0-0c7146d

Render an rmarkdown notebook. Supports parametrization.

R notebook reports

Latest version: 0.0.0-0c7146d

Total downloads: 1

Source: nf-core/modules

Authors: @grst

Maintainers: @grst

Render an rmarkdown notebook. Supports parametrization.

Add the following snippet to your workflow script to include this module.

include { RMARKDOWNNOTEBOOK } from 'nf-core/rmarkdownnotebook'

MIT License

Process

`Name`	`RMARKDOWNNOTEBOOK`

Input 3 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`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 5 channels

#1 report tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.html` file	HTML report generated from Rmarkdown `*.html`

#2 versions

`versions.yml` file	File containing software versions `versions.yml`

#3 artifacts tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`artifacts/*` file	Artifacts generated by the notebook `artifacts/*`

#4 session_info tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`session_info.log` file	dump of R SessionInfo `*.log`

#5 parameterised_notebook tuple

`meta` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`*.parameterised.Rmd` file	Parameterised Rmarkdown file `*.parameterised.Rmd`

Tool	Description	Homepage
rmarkdown	Dynamic Documents for R	https://rmarkdown.rstudio.com/

Version	0.0.0-0c7146d
Commit ID	135d883a43b1a2324b4112cd270cf22e20835533
Release Date	08 Apr 2026 19:08:19 (UTC)
Download URL	https://registry-stage.nextflow.io/api/v1/modules/nf-core%2Frmarkdownnotebook/0.0.0-0c7146d/download
OCI Store URL	https://public.cr.stage-seqera.io/v2/nextflow/plugin-stage/modules/nf-core/rmarkdownnotebook/blobs/sha256:4d2015ec18f757b43bf4bad82a2f02e4532cdee7306bf5a8a9bfc4c62c87e695
Size	3.9 KB
Checksum	sha256:4d2015ec18f757b43bf4bad82a2f02e4532cdee7306bf5a8a9bfc4c62c87e695
Downloads	1

Version	Date	Status	Downloads	Size	Diff
0.0.0-0c7146d	08 Apr 2026 19:08:19 (UTC)		1	3.9 KB	-