bio-reporting-jupyter-reports - Parameterized Jupyter Notebook Report Generation
Runs parameterized Jupyter notebooks using Papermill, renders HTML/PDF reports with nbconvert, and aggregates cohort results.
Tags
Updated: 2026-09-24Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Execute parameterized notebooks with Papermill
- Render notebooks to HTML and PDF
- Aggregate notebook metrics with Scrapbook
- Strip notebook outputs with nbstripout
Inputs
- Jupyter notebook templates
- Execution parameters
- Sample datasets
Outputs
- Executed notebook files
- Rendered HTML reports
- Rendered PDF reports
- Aggregated data tables
Requirements
- Python runtime environment
- papermill 2.6+
- nbconvert 7.16+
- Registered Jupyter kernel