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🔧 Configuration

The configuration file serves as the central blueprint for the PlexPipe analysis. It provides parameters for all stages of the pipeline divided into sections corresponding to the analysis steps.

This configuration is defined in a YAML file; you can find a deep dive into the syntax at YAML official website, but the description and examples below should be more than enough to get you started.

Reproducibility and Provenance

To maintain a reliable audit trail, avoid modifying parameters once a step has been completed. The configuration file, paired with the resulting log files, serves as the formal documentation for the pipeline execution.

Config Validation

To ensure your configuration is valid, the system validates your input against a predefined schema.

Validation Rules:

  • Required Fields: These must be present in your configuration file. If a required field is missing, the application will return an error.

  • Optional Fields: These are labeled as (optional). You can choose to:

    • Omit them entirely (the system will use its default behavior).
    • Set them to null (or ~) to explicitly signify no custom value.
    • Provide a custom value to override the default.

Path Format

When entering file paths in this configuration file, always use the forward slash (/) as the folder separator, even on Windows. The backslash (\) is a "special character" in YAML. Using it can cause errors or require you to "double-up" your slashes (e.g., C:\\Users).

Correct: C:/path/to/images Avoid: C:\path\to\images.

Examples

Full example configuration files can be found in the examples folder.