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/example_inputs.py

@@ -0,0 +1,37 @@
+# Copyright (c) 2024 Chai Discovery, Inc.
+
+# Licensed under the Apache License, Version 2.0.
+# See the LICENSE file for details.
+
+example_ligands = [
+    "C",
+    "O",
+    "C(C1C(C(C(C(O1)O)O)O)O)O",
+    "[O-]S(=O)(=O)[O-]",
+    "CC1=C(C(CCC1)(C)C)/C=C/C(=C/C=C/C(=C/C=O)/C)/C",
+    "CCC1=C(c2cc3c(c(c4n3[Mg]56[n+]2c1cc7n5c8c(c9[n+]6c(c4)C(C9CCC(=O)OC/C=C(\C)/CCC[C@H](C)CCC[C@H](C)CCCC(C)C)C)[C@H](C(=O)c8c7C)C(=O)OC)C)C=C)C=O",
+    r"C=CC1=C(C)/C2=C/c3c(C)c(CCC(=O)O)c4n3[Fe@TB16]35<-N2=C1/C=c1/c(C)c(C=C)/c(n13)=C/C1=N->5/C(=C\4)C(CCC(=O)O)=C1C",
+    # different ions
+    "[Mg+2]",
+    "[Na+]",
+    "[Cl-]",
+]
+
+example_proteins = [
+    "AGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVR",
+    "(KCJ)(SEP)(PPN)(B3S)(BAL)(PPN)K(NH2)",
+    "XDHPX",
+]
+
+
+example_rna = [
+    "AGUGGCUA",
+    "AAAAAA",
+    "AGUC",
+]
+
+example_dna = [
+    "AGTGGCTA",
+    "AAAAAA",
+    "AGTC",
+]