.coverage
.codex
.DS_Store
.ipynb_checkpoints/
.pytest_cache
.vscode
*.bam*
*.fastq.gz
*.log
# Python
__pycache__/
*.py[cod]
*$py.class
*.so
.Python
*.egg
*.egg-info/
dist/
build/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.manifest
*.spec

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

# Testing
.pytest_cache/
.coverage
.coverage.*
htmlcov/
.tox/
.nox/
*.cover
.hypothesis/
pytestdebug.log

# IDEs
.vscode/
.idea/
*.swp
*.swo
*~
.project
.pydevproject
.settings/

# Jupyter Notebook
.ipynb_checkpoints/
*.ipynb_checkpoints/
check_config.ipynb
check_design.ipynb
check_outputs.ipynb
fastq_class_sandbox.ipynb
test_rna_size_factors.ipynb

# macOS
.DS_Store
.AppleDouble
.LSOverride
._*

# Documentation builds
site/
docs/_build/
old_docs/

# Logs
*.log
logs/

# Distribution / packaging specific
**/__pycache__
**/.pyc

# Project-specific
*.bam*
*.fastq.gz
*.sif
*.tar
*.tar.gz
**.bt2
**.egg-info
**/__pycache__
**/.pyc
**GenomeDir
*delete*
*egg*
*target/*
202*
build/*
check_config.ipynb
check_design.ipynb
check_outputs.ipynb
containers/*.sif
containers/push_notes.txt
design_test/metadata_chip.csv
dist/*
fastq_class_sandbox.ipynb
htmlcov
metadata.csv
output.yml
paths.txt
pytestdebug.log
seqnado/_version.py
sps*
test_run.sh
test.json
test_output
**GenomeDir
*delete*
*target/*
202*
containers/*.sif
containers/push_notes.txt
design_test/metadata_chip.csv
lolcow.sif
metadata.csv
ngs_pipeline/tests/pipeline/
output.yml
paths.txt
seqnado/_version.py
snakefiles_old
sps*
test_output/
test_run.sh
test.json
testing
tests/data*
tests/make_data*

# Temporary files
*.tmp
*.temp
*.cache
testing_dir/
update_test_data.ipynb
seqnado/workflow/rules/genomes/scripts
.snakemake/
.claude/settings.json
quantnado.ipynb