Update README with expected output file names, clean up snakemake scr…#4

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cdbope merged 1 commit intomasterfrom

update-readme-and-scripts

Jul 25, 2025

Commits on Jul 25, 2025

Update README with expected output file names, clean up snakemake scripts with proper documentation, and fix indentation issues in main_fixed_denovo.py
cdbope
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