Rename repo from flu-syn-rates to flu-mut-rates in docs

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: Haddox

CLAUDE.md

@@ -8,7 +8,7 @@ This file provides guidance to Claude Code (claude.ai/code) when working with co
 
 ## Project Overview
 
-Flu-syn-rates - A Snakemake pipeline for analyzing synonymous and non-synonymous mutation rates in influenza virus phylogenetic trees. The pipeline processes mutation patterns across different influenza segments and subtypes, calculating mutation counts and rates from phylogenetic trees generated by flu-usher.
+Flu-mut-rates - A Snakemake pipeline for analyzing synonymous and non-synonymous mutation rates in influenza virus phylogenetic trees. The pipeline processes mutation patterns across different influenza segments and subtypes, calculating mutation counts and rates from phylogenetic trees generated by flu-usher.
 
 ## Key Commands
 

README.md

@@ -1,4 +1,4 @@
-# flu-syn-rates
+# flu-mut-rates
 
 ## Overview
 
@@ -9,7 +9,7 @@ This pipeline calculates synonymous and non-synonymous mutation rates across inf
 ### Directory Structure
 
 ```
-flu-syn-rates/
+flu-mut-rates/
 ├── Snakefile             # Main workflow definition
 ├── config.yaml           # Configuration file
 ├── scripts/