# Python bytecode / test & lint caches
__pycache__/
*.py[cod]
.pytest_cache/
.ruff_cache/

# Nextflow run state. The wrapper launches Nextflow with cwd = the user's
# --output directory (never here); these guard against stray dev runs inside
# the skill leaking framework bookkeeping into the repo.
.nextflow/
.nextflow.log
work/

# Run outputs: the wrapper writes results and the reproducibility bundle to the
# --output directory, not into the skill. (The tracked reproducibility/*.json
# files are shipped reference data, not run output.)
output/

# macOS
.DS_Store
