# Python development
__pycache__/
*.py[cod]
*$py.class
uv*
*.ruff_cache

# Distribution
.Python
build/
dist/
*.egg-info/
nosetests.xml
coverage.xml
*.cover
*.square
*container*

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

# Testing
.pytest_cache/
.tox/
.coverage
htmlcov/
*png
*ank*
*plan*
*docs*
.maggic-wand

# Pipeline outputs and temporary files
IN-LS/
work/
.nextflow.log*
.nextflow/
slurm-*.out
job_scripts/
resolve-fastq/
results_*/
CPIPES-bettercallsal/
bettercallsal/
fastq_json_cache/
bactree-tests/__pycache*
*rules*

# IDEs and Editors
.vscode/
.idea/
*.swp
*.swo
.DS_Store

# Local environment/config
.env
.env.*
*bank/*
