bio-reporting-jupyter-reports

name	bio-reporting-jupyter-reports
description	Creates reproducible Jupyter notebooks for bioinformatics analysis with parameterization using papermill. Use when generating automated analysis reports, running notebook-based pipelines, or creating shareable computational notebooks.
tool_type	python
primary_tool	papermill

Jupyter Reports with Papermill

Parameterized Notebooks

import papermill as pm

# Execute notebook with parameters
pm.execute_notebook(
    'analysis_template.ipynb',
    'output_report.ipynb',
    parameters={
        'input_file': 'data/counts.csv',
        'condition_col': 'treatment',
        'fdr_threshold': 0.05
    }
)

Creating Parameterized Templates

Mark a cell with the parameters tag in Jupyter:

# Parameters (tag this cell as "parameters")
input_file = 'default.csv'
output_dir = 'results/'
fdr_threshold =