# env 
.venv/

# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
env/
venv/
ENV/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST
*.whl
.pypirc

# Jupyter Notebook
.ipynb_checkpoints
*.ipynb

# Virtual environments
.env
.venv
env/
venv/

# IDE
.vscode/
.idea/
*.swp
*.swo
*~

# Log files
*.log
*.out

# Data files - sequencing and analysis outputs
*.tar
*.tar.gz
*.tar.md5
*.md5
*.h5
*.bam
*.bam.bai
*.fastq
*.fastq.gz
*.fq
*.fq.gz

# Analysis directories and outputs
Unaligned/
Analysis_*/
Flowcell_*/
**/molecule_info.h5
**/star_out.bam
**/barcodes/
**/cell_calling/
**/clustering/
**/filtered_matrix/
**/raw_matrix/
**/star/
**/logs/
**/metrics/
**/cache/**
test.loom

# Error logs and reports
*errorLog*.txt
*errorRecords*.txt

# Slurm output files
slurm-*.out

# OS files
.DS_Store
Thumbs.db

# Temporary files
*.tmp
*.temp
