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

]

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

meta (map)

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

]

report (file)

HTML report generated from Jupyter notebook

*.html

versions (file)

File containing software versions

versions.yml
author
Github user grst
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Tools

jupytext
MIT

Jupyter notebooks as plain text scripts or markdown documents

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

papermill
BSD 3-clause

Parameterize, execute, and analyze notebooks

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

nbconvert
BSD 3-clause

Parameterize, execute, and analyze notebooks

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