# Python
__pycache__/
*.py[cod]
*$py.class
.pytest_cache/
.mypy_cache/
.ruff_cache/
.coverage
htmlcov/
*.egg-info/
.eggs/
dist/
build/
*.egg

# Virtual environments
.venv/
venv/
.mamba/

# IDE
.vscode/
.idea/
*.swp
*.swo

# OS
.DS_Store
Thumbs.db

# Project-specific
resources/*
!resources/.gitkeep
results/*
!results/.gitkeep
log/*
!log/.gitkeep
*.log
progress.json
progress.jsonl
.abi/
abi_workspace/
workspace/
work/
.nextflow/
.nextflow.log*
nextflow_work/
nf_work/
job_store.json
jobs.json

# Ignore user data by default, but keep curated small examples.
data/*
!data/examples/
!data/examples/**

# Large sequencing or archive inputs should not be committed by default.
*.bam
*.bai
*.sam
*.cram
*.fastq
*.fq
*.fastq.gz
*.fq.gz
*.fasta.gz
*.fa.gz
*.tar
*.tar.gz
*.tgz
*.zip
*.7z

# Keep intentionally tiny test fixtures.
!examples/fixtures/**
!tests/fixtures/**

# CMake (if used)
CMakeCache.txt
CMakeFiles/
cmake_install.cmake
Makefile
CTestTestfile.cmake
Testing/
