Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

notebook{:bash}

:file

Jupyter notebook or jupytext representation thereof

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

parameters{:bash}

:map

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

input_files{:bash}

:file

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

*

Output

name:type
description
pattern

report{:bash}

meta{:bash}

:map

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

*.html{:bash}

:file

HTML report generated from Jupyter notebook

*.html

artifacts{:bash}

meta{:bash}

:map

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

artifacts/{:bash}

:directory

Directory containing all artifacts generated by the notebook

artifacts/

versions{:bash}

versions.yml{:bash}

: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/

nbconvert

Parameterize, execute, and analyze notebooks

nbconvert.readthedocs.io/en/latest https://github.com/jupyter/nbconvert
maintainer
Github user grst
get in touch
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