# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# Virtual environments
venv/
ENV/
env/
.venv

# Testing
.pytest_cache/
.coverage
htmlcov/
.tox/
.hypothesis/

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

# OS
.DS_Store
Thumbs.db

# Project specific
*.fastq.gz
*.bam
*.sam
*_fastqc/
*_fastqc.html
*_fastqc.zip
multiqc_data/
multiqc_report.html
batch_output/
test_output/
pipeline_output/

# Temporary files
*.log
*.json
*.csv
*.md
!README.md
!LICENSE

# Test data (except sample test data)
real_test_data/
test_chipseq_qc/
test_rnaseq_final/
chipseq_qc/
rnaseq_qc/
combined_qc/
test_sample_fastqc/
