Documenting your analysis

Each analysis module should include a README.md file with important information about the analysis and instructions for running the analysis module. This file can be particularly helpful to other contributors who want to use your analysis module and to you when you revisit a module you've written in the past.

We have provided a template README.md that will be automatically included when you create a new analysis module. You should fill out the template for your analysis module and provide the following information for each analysis:

• Description of module goals
• Usage (How to run the analysis)
• Input files and their sources. These may include:
  • ScPCA data files and/or result files from other modules. (See access instructions.)
  • External data including links to their origins.
• Output files
• Software and package dependencies
• Computational resources

For some examples of analysis module README.md files, please see our example R module and/or our example Python module.

We recommend that as you continue to work on the analysis, you update the README.md file with each change. For example, if you add a new step in the analysis module, your pull request should include the code changes and an update to the README.md containing a description of that step.

Documentation is just as important as your code! The Data Lab will not approve pull requests without proper documentation.

Is this your first analysis module?

If you are creating your first analysis module, we recommend that you scope your first pull request to contain only:

• The analysis module skeleton created by running create-analysis-module.py
• A README.md file containing at minimum, a description of the analysis
  • Other headers in the README.md, like Usage, can be filled out as the analysis proceeds