Wrapped scripts in Snakemake, added SLURM configuration, and revised the variant generation logic.

This merge request overhauls the repo. Scripts are now wrapped in a Snakemake rule that automates everything: generating a graph, FASTA, and VCF. The VG pipeline is added, and the workflow now runs on SLURM-enabled HPCs. The variant generation script is also rewritten in OOP style.