BDB-Genomics CUT&RUN Pipeline

A production-grade, config-driven Snakemake framework for CUT&RUN sequencing data analysis. Built for resilience, it handles the full lifecycle from raw FASTQ reads through alignment, spike-in calibration, peak calling, and differential binding analysis.

🚀 Quick Start

1. Configure: Edit config.yaml and provide metadata in data/samples.tsv.
2. Execute: Run via the automated wrapper scripts.

   # Run locally (8 cores)
   scripts/run_pipeline.sh -c 8 -- --profile profiles/local
   
   # Run on HPC (SLURM)
   scripts/run_pipeline.sh -- --profile profiles/slurm

📁 Repository Structure

• profiles/ - Execution profiles (Local, SLURM, GCP)
• scripts/ - Pipeline execution wrappers
• rules/ - Modular Snakemake rules and isolated conda environments
• AGENTS.md - Agent context and knowledge base index

For comprehensive documentation, see the README.md files in each sub-directory or the OpenWiki documentation.