# Docker
.dockerignore

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

# Genome files (large)
genome/
*.fa
*.fa.fai
*.ht2
*.ss

# Track files (large)
*.bb
*.bw
*.bigWig
*.bigBed

# 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/

# Jupyter
.ipynb_checkpoints/
*.ipynb_checkpoints

# Results and outputs
results/
output/
test_out/
*_output/
deprecated_v1_*/

# Logs
*.log
run.log
*.out.txt
*.err.txt

# Data files
*.bam
*.sam
*.bai
*.cram
*.fastq
*.fastq.gz
*.fq
*.fq.gz
*.sra

# Temporary files
tmp/
temp/
.snakemake/

# OS
.DS_Store
Thumbs.db

# MLflow
mlruns/
mlflow.db

# Backup files
*.bak
*.backup
*~
*.old
deprecated_*
