implement MitSorter tool for mtDNA focused analyses

Issue

With the evolution, a few fragments of mtDNA were inserted into nDNA. They are called nuclear mitochondrial DNA segments (NuMTs), and this produces misalignments that can bias modkit analyses and/or dorado/minimap2 to map these NuMTs instead of the true mitochondrial genome. Based on this, our pipeline might benefit from including the MitSorter tool as an optional choice for the user. The tool can discriminate between mtDNA and NuMTs, which provides an accurate data analysis down the line. You can find the research paper about the tool here: https://pmc.ncbi.nlm.nih.gov/articles/PMC12275464/

New Issue if we consider implementation

The MitSorter is available as a Snakemake customizable pipeline: https://github.com/asvarvara/MitSorter

We'll need to discuss how to implement it and whether this will cause any conflicts with Nexflow. Also, we need to look into whether conda must be available inside the container for the tool to work.