gbcms/.gitignore at main · msk-access/gbcms · GitHub

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# 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

# Virtual environments
venv/
env/
ENV/
.venv

# Testing
.pytest_cache/
.coverage
htmlcov/
.tox/
coverage.xml
*.cover
.mypy_cache/
.ruff_cache/
.benchmarks/

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

# OS
.DS_Store
Thumbs.db

# Project specific
data/
test_data/
*.bam
*.bam.bai
*.fa
*.fa.fai
*.vcf
*.maf
*.parquet
*.mfsd_report.html
output/
results/
test_output*/
*.txt
scripts/*_test/

# Exception: Allow test data files
!tests/testdata/*.bam
!tests/testdata/*.bam.bai
!tests/testdata/*.fa
!tests/testdata/*.fa.fai
!tests/testdata/*.vcf
!tests/testdata/*.maf
!tests/testdata/*.parquet

# Logs
*.log

# Temporary files
tmp/
temp/
debug_*.py
validate_*.py

# Rust
target/

# Nextflow
.nextflow/
.nextflow.log*
work/
test_results*/
test_rwd/
test_samplesheet*.csv

# Documentation
site/
docs/assets/images/*_mermaid_*.svg

# Ad-hoc analysis scripts
scratch/
mfsd_review_report.html