Workflow
=========

This Snakemake workflow automates the extraction of epigenomic features using Finaletoolkit, supporting parallel processing, SLURM, and common genomic file formats. You can find and access the workflow `here <https://github.com/epifluidlab/finaletoolkit_workflow>`_.

.. toctree::
   :maxdepth: 2
   :caption: Contents:

   key_features
   installation
   dependencies
   quick_start
   workflow_structure
   yaml_parameters
   output_file_naming
   finaletoolkit_commands
   mappability_filtering
   filter_file
   notes