Add bash script for running CellBender ambient RNA removal

[Copilot]

Overview

This PR adds a bash script and comprehensive documentation for running CellBender, a tool for removing ambient RNA contamination from single-cell RNA-seq data.

Changes

New Files

1. scripts/run_cellbender.sh - Production-ready bash script with:

   • User-friendly command-line interface with both short and long options
   • Required parameters: input file, output directory, expected cells, total droplets
   • Optional parameters: FPR, epochs, CUDA support, learning rate, latent dimensions, and more
   • Built-in help documentation with usage examples
   • Comprehensive error handling and input validation
   • Proper exit codes and informative error messages

2. docs/usage_cellbender.md - Complete documentation including:

   • Explanation of ambient RNA and why removal is important
   • Installation instructions for CellBender
   • Detailed parameter guidance and best practices
   • Multiple usage examples (basic, GPU-accelerated, custom parameters)
   • Integration instructions for using CellBender output with Seurat
   • Troubleshooting section for common issues
   • References to CellBender paper and documentation

Usage Example

./scripts/run_cellbender.sh \
    --input raw_feature_bc_matrix.h5 \
    --output-dir cellbender_output \
    --expected-cells 5000 \
    --total-droplets 15000 \
    --cuda

Quality Assurance

• ✅ Script passes shellcheck validation with no warnings
• ✅ Comprehensive error handling for missing/invalid inputs
• ✅ Follows bash best practices (set -euo pipefail, proper quoting)
• ✅ Executable permissions set correctly
• ✅ Help text provides clear usage instructions

Benefits

• Provides a standardized way to run CellBender in the scrnaseq2 workflow
• Simplifies ambient RNA removal for users unfamiliar with CellBender CLI
• Comprehensive documentation reduces setup friction and troubleshooting time
• Consistent with the project's focus on best practices for single-cell analysis

Original prompt

Create bash script for running cellbender

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