AI-Genomics-Lab/.gitignore at main · rendergraf/AI-Genomics-Lab · GitHub

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# ============================================
# 🧬 AI Genomics Lab - .gitignore
# ============================================

# ============================================
# Environment Variables
# ============================================
.env
.env.local
.env.production
.env*.local

# ============================================
# 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

# Dependency lock files
Pipfile.lock
poetry.lock
requirements-dev.txt
dev-requirements.txt
requirements-*.txt
!requirements.txt

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

# PyCharm
.idea/

# VS Code
.vscode/

# Jupyter Notebook
.ipynb_checkpoints

# ============================================
# Nextflow
# ============================================
.nextflow/
.nextflow.log*
nextflow-work/
.nextflow/history
nextflow.history
nextflow.config.local
nextflow.config.*
!nextflow.config
.nextflow/asset/*
.nextflow/cache/*
work/
*.nextflow.log
nextflow
pipeline_reports/
reports/
pipeline_trace.txt
pipeline_timeline.html
pipeline_report.html
bio-pipeline/report-*.html

# ============================================
# Node.js
# ============================================
node_modules/
npm-debug.log*
yarn-debug.log*
yarn-error.log*
.npm
.yarn-integrity

# Next.js
.next/
out/
.vercel

# ============================================
# Docker
# ============================================
.docker/
docker-compose.override.yml
docker-compose.local.yml
docker-compose.dev.yml
docker-compose.prod.yml
docker-compose.test.yml
docker-compose.*.yml
!docker-compose.yml

# ============================================
# Data Files (Sensitive)
# ============================================
datasets/**
!datasets/.gitkeep
reference_genome/
*.fastq
*.fq
*.fasta
*.fa
*.bam
*.sam
*.vcf
*.vcf.gz
*.bed
*.bcf

# Genome index files
*.fai
*.gzi
*.sti
*.fa.gz
*.fa.gz.fai
*.fa.gz.gzi
*.fa.gz.sti
*.r150.sti

# Database files
*.db
*.sqlite
*.sqlite3
neo4j-data/
minio-data/
*.sql
*.sql.gz
*.dump

# ============================================
# Logs
# ============================================
logs/
*.log
npm-debug.log*

# ============================================
# OS
# ============================================
.DS_Store
Thumbs.db

# ============================================
# Testing
# ============================================
.coverage
htmlcov/
.pytest_cache/
.mypy_cache/

# ============================================
# Temporary Files
# ============================================
tmp/
temp/
*.tmp
*.swp
*.swo
*~

# ============================================
# Secrets & Keys (CRITICAL)
# ============================================
*.pem
*.key
*.crt
credentials.json
service-account.json

# ============================================
# Local Configuration
# ============================================
config.local.yaml
config.local.yml
settings.local.py
local_settings.py
.env.local
.env.development
.env.test
.env.production.local

# ============================================
# Documentation Build
# ============================================
site/
docs/_build/

*storybook.log
storybook-static