Initial commit: Chai-1 protein structure prediction pipeline for WES

- Nextflow pipeline using chai1 Docker image from Harbor
- S3-based input/output paths (s3://omic/eureka/chai-lab/)
- GPU-accelerated protein folding with MSA support

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

pyproject.toml

@@ -0,0 +1,74 @@
+# important: install in editable mode
+[build-system]
+requires = [
+    "hatchling>=1.20",        # build backend
+    "hatch-requirements-txt", # plugin, to parse requirements.txt
+]
+build-backend = "hatchling.build"
+
+
+[project]
+name = "chai_lab"
+description = "Chai Discovery tools for AI + protein research."
+requires-python = ">=3.10"
+authors = [{ name = "Chai Discovery" }]
+# see both defined below
+dynamic = ["version", "dependencies"]
+
+[tool.hatch.version]
+path = "chai_lab/__init__.py"
+[tool.hatch.metadata.hooks.requirements_txt]
+files = ["requirements.in"]
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.mypy]
+check_untyped_defs = true
+
+# Ignore missing imports for packages with missing type stubs
+[[tool.mypy.overrides]]
+module = [
+    "anarci.*",
+    "fsspec.*",
+    "google.*",
+    "joblib.*",
+    "needletail.*",
+    "numba.*",
+    "pyximport.*",
+    "rdkit.*",
+    "scipy.*",
+    "seaborn.*",
+    "sh.*",
+    "tmtools.*",
+    "botocore.*",
+    "s3fs.*",
+    "biotite.*",
+    "DockQ.*",
+    "boto3.*",
+    "transformers.*",
+    "modelcif.*",
+    "ihm.*",
+]
+ignore_missing_imports = true
+
+[tool.pytest.ini_options]
+cache_dir = "/tmp/.common_pytest_cache"
+
+
+[tool.hatch.build.targets.sdist]
+exclude = [
+    "/.devcontainer",
+    "/.github",
+    "/.idea",
+    "/.vscode",
+    "/.pytest_cache",
+    "/assets",
+    "/downloads",
+    "/outputs",
+]
+
+[tool.hatch.build.targets.wheel]
+# should use packages from sdist section
+
+[project.scripts]
+chai = "chai_lab.main:cli"