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CLAUDE.md

This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.

IMPORTANT: Always read AGENTS.md at the start of every session before doing any work. It contains comprehensive project context and development guidelines that are essential for working in this codebase.

Quick Reference

  • Docker-centric development: Run tests inside containers, not on host
  • Import pattern: from viral_ngs import core then core.samtools.SamtoolsTool()
  • Test location: tests/unit/<module>/
  • Dependencies: ALL via conda, not pip (see docker/requirements/*.txt)

Running Tests

docker run --rm \
  -v $(pwd):/opt/viral-ngs/source \
  quay.io/broadinstitute/viral-ngs:main-core \
  pytest -rsxX -n auto /opt/viral-ngs/source/tests/unit

Key Files

File Purpose
AGENTS.md Full AI assistant guidance
pyproject.toml Package configuration
docker/ Dockerfiles and requirements
src/viral_ngs/ Source code
tests/ Test files
.agents/skills/ Reusable agent playbooks and scripts