name: jupyternotebook
description: |
  Render jupyter (or jupytext) notebooks to HTML reports. Supports parametrization
  through papermill.
keywords:
  - Python
  - Jupyter
  - jupytext
  - papermill
  - notebook
  - reports
tools:
  - jupytext:
      description: Jupyter notebooks as plain text scripts or markdown documents
      homepage: https://github.com/mwouts/jupytext/
      documentation: https://jupyter.org/documentation
      tool_dev_url: https://github.com/mwouts/jupytext/
      licence: "MIT"
  - papermill:
      description: Parameterize, execute, and analyze notebooks
      homepage: https://github.com/nteract/papermill
      documentation: http://papermill.readthedocs.io/en/latest/
      tool_dev_url: https://github.com/nteract/papermill
      licence: "BSD 3-clause"
  - nbconvert:
      description: Parameterize, execute, and analyze notebooks
      homepage: https://nbconvert.readthedocs.io/en/latest/
      documentation: https://nbconvert.readthedocs.io/en/latest/
      tool_dev_url: https://github.com/jupyter/nbconvert
      licence: "BSD 3-clause"

input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - notebook:
      type: file
      description: Jupyter notebook or jupytext representation thereof
      pattern: "*.{ipynb,py,md,Rmd,myst}"
  - parameters:
      type: map
      description: |
        Groovy map with notebook parameters which will be passed
        to papermill in order to create parametrized reports.
  - input_files:
      type: path
      description: One or multiple files serving as input data for the notebook.
      pattern: "*"

output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - report:
      type: file
      description: HTML report generated from Jupyter notebook
      pattern: "*.html"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"

authors:
  - "@grst"