setup.sh runs install steps; Snakefile has working example rules#3
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- setup.sh now runs uv sync, copies config template to config.yaml, and installs pre-commit hooks after prerequisite checks pass - Replace commented-out Snakefile placeholder with functional example rules (process_data, summarize) that use config.yaml - Add example workflow scripts (process_data.py, summarize.py) so the pipeline is runnable out of the box https://claude.ai/code/session_012TNv3qDVee7nBFUViVtRvM
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https://claude.ai/code/session_012TNv3qDVee7nBFUViVtRvM