Codon usage and go enrichment pipeline

Created by: oliverbader

Implement CUG-clade specific genetic code handling for codon usage analysis.

The CUG-clade genetic code is a known biological deviation where the CTG codon translates to Serine instead of Leucine. This PR introduces a flag and configuration option to switch to this alternative genetic code, ensuring accurate codon usage calculation and downstream GO enrichment analysis for these fungal species.