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>

tests/test_rdkit.py

@@ -0,0 +1,24 @@
+# Copyright (c) 2024 Chai Discovery, Inc.
+# Licensed under the Apache License, Version 2.0.
+# See the LICENSE file for details.
+
+from chai_lab.data.sources.rdkit import RefConformerGenerator
+
+
+def test_ref_conformer_from_smiles():
+    """Test ref conformer generation from SMILES."""
+    smiles = "Cc1cc2nc3c(=O)[nH]c(=O)nc-3n(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1C"
+    rcg = RefConformerGenerator()
+
+    conformer = rcg.generate(smiles)
+
+    assert len(set(conformer.atom_names)) == conformer.num_atoms
+
+
+def test_ref_conformer_glycan_ccd():
+    """Ref conformer from CCD code for a sugar ring."""
+    rcg = RefConformerGenerator()
+    conformer = rcg.get("MAN")
+    assert conformer is not None
+
+    assert len(set(conformer.atom_names)) == conformer.num_atoms