modules/jupyternotebook

Render jupyter (or jupytext) notebooks to HTML reports. Supports parametrization through papermill.

PythonJupyterjupytextpapermillnotebookreports

https://github.com/nf-core/modules/[...]/modules/nf-core/jupyternotebook

Description

Render jupyter (or jupytext) notebooks to HTML reports. Supports parametrization through papermill.

Input

name:type

description

pattern

`meta:map`

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

`notebook:file`

Jupyter notebook or jupytext representation thereof

*.{ipynb,py,md,Rmd,myst}

`parameters:map`

Groovy map with notebook parameters which will be passed to papermill in order to create parametrized reports.

`input_files:file`

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

*

Output

name:type

description

pattern

`report`

`meta:map`

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

`*.html:file`

HTML report generated from Jupyter notebook

*.html

`artifacts`

`meta:map`

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

`artifacts/:directory`

Directory containing all artifacts generated by the notebook

artifacts/

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

jupytext

Jupyter notebooks as plain text scripts or markdown documents

github.com/mwouts/jupytext jupyter.org/documentation https://github.com/mwouts/jupytext/

papermill

Parameterize, execute, and analyze notebooks

github.com/nteract/papermill http://papermill.readthedocs.io/en/latest https://github.com/nteract/papermill

nbconvert

Parameterize, execute, and analyze notebooks

nbconvert.readthedocs.io/en/latest https://github.com/jupyter/nbconvert