# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
.hypothesis/
.pytest_cache/

# Virtual environments
.env
.venv/
env/
venv/
ENV/
env.bak/
venv.bak/
.pip/

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

# OS
.DS_Store
Thumbs.db

# Project specific
cache/
*.log
results/
output/
temp/
tmp/

# Nextflow
.nextflow/
.nextflow.log*
work/
.nextflow_work/

# Docker
.dockerignore

# Development
.mypy_cache/
.ruff_cache/

# Documentation
docs/_build/

# Test artifacts
.pytest_tmp/
nextflow_work/
nxf-tmp.*
pytest-report.xml
pytest-*-report.xml
pytest-container-report.xml
pytest-host-report.xml

# Workflow debug outputs (generated by tests / local runs)
workflow_test_debug_*/
tp53_workflow_debug/
workflow_output/
docker_results/
