add example configurations, annotations, data and results to all modules

[sreichl]

Provide small example data, configs, annot and results for each module by copying from one fitting recipe and pointing there for context and biological interpretation.

• Think about a fitting setup for all modules
• add example annotation.csv to every module config/ for human and AI to understand -> copy from recipe

[sreichl]

Data Organization and Structure

• Recipe Integration: Example and test data should be derived directly from recipe outputs to ensure consistency.
• Standardized Directory Hierarchy: Implement a uniform folder structure using a primary test directory containing subfolders for data (counts/annotations), config (configuration files), and results (output).
• Documentation and Referencing: Each dataset must include a simple description and a direct link to its source recipe.

User Accessibility and Support

• Execution Commands: Provide explicit commands to run examples, allowing users to verify module functionality immediately.
• Extended Documentation: Direct users to the main repository Wiki for comprehensive details on module application within larger project contexts.

Challenges with Large Datasets

• Module Constraints: Large data requirements for quantification (TACSIC RNA), genome tracks, and single-cell modules present storage and handling difficulties.
• Potential Solutions:
• Remote Sourcing: Transitioning from local file paths to URL or Zenodo-hosted inputs to maintain module integrity.
• Data Down-sampling: Using reduced datasets, acknowledging that this may limit the depth of biological feature testing.

Development and Integration Goals

• Continuous Improvement: Integrating tests and examples is vital for ongoing development, integration testing, and system maintenance.
• Onboarding: Providing accessible test data lowers the entry barrier for new users, facilitating easier adoption of the tools.

[sreichl]

Consider using this for genetic test data: https://github.com/snakemake-workflows/ngs-test-data

or just take (subsets) of intermediate results from MrBiomics paper directly.