Workflow Structure
------------------

*   **Input:**

    *   Genomic data files are located in the directory specified by ``input_dir``.
    *   Supplemental files (blacklist, mappability, intervals) are located in the directory specified by ``supplement_dir``.
*   **Output:** Processed files are written to the directory specified by ``output_dir``.
*   **Configuration:** ``params.yaml`` dictates workflow parameters.