Nextflow Registry | nf-core/quartonotebook@0.0.0-6c4ed3a

nf-core/quartonotebook @ 0.0.0-6c4ed3a

Render a Quarto notebook, including parametrization.

quarto notebook reports python r

Latest version: 0.0.0-6c4ed3a

Total downloads: 7

Source: nf-core/modules

Authors: @fasterius

Maintainers: @fasterius

Render a Quarto notebook, including parametrization.

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

include { QUARTONOTEBOOK } from 'nf-core/quartonotebook'

MIT License

Process

`Name`	`QUARTONOTEBOOK`

Input 4 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`.
`notebook` file	The Quarto notebook to be rendered. `*.{qmd}`

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

`input_files` file	One or multiple files serving as input data for the notebook. `*`

`extensions` file	A quarto `_extensions` directory with custom template(s) to be available for rendering. `*`

Output 7 channels

#1 html tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`.
`*.html` file	HTML report generated by Quarto. `*.html`

#2 notebook tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`.
`notebook` file	The Quarto notebook that was rendered. Allows user to continue working on the notebook. `*.{qmd}`

#3 artifacts tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`.
`${notebook_parameters.artifact_dir}/*` file	Artifacts generated during report rendering. `*`

#4 extensions tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`.
`_extensions` file	Quarto extensions used during report rendering. `*`

#5 params_yaml tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`.
`params.yml` file	Parameters used during report rendering. `*`

#6 versions_quarto tuple

`${task.process}` string	The name of the process
`quarto` string	The name of the tool
`quarto -v` eval	The expression to obtain the version of the tool

#7 versions_papermill tuple

`${task.process}` string	The name of the process
`papermill` string	The name of the tool
`papermill --version \| cut -f1 -d" "` eval	The expression to obtain the version of the tool

Tool	Description	Homepage
quartonotebook	An open-source scientific and technical publishing system.	https://quarto.org/
papermill	Parameterize, execute, and analyze notebooks	https://github.com/nteract/papermill

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b
Release Date	23 Apr 2026 15:39:25 (UTC)
Download URL	https://registry.nextflow.io/api/v1/modules/nf-core%2Fquartonotebook/0.0.0-6c4ed3a/download