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>

params.json

@@ -0,0 +1,83 @@
+{
+    "params": {
+        "input_dir": {
+            "type": "folder",
+            "description": "Directory containing FASTA files and optional restraints",
+            "default": "s3://omic/eureka/chai-lab/input",
+            "required": true,
+            "pipeline_io": "input",
+            "var_name": "params.input_dir",
+            "examples": [
+                "s3://omic/eureka/chai-lab/input"
+            ],
+            "pattern": ".*",
+            "enum": [],
+            "validation": {},
+            "notes": "Directory containing FASTA files (with *_complex.fasta suffix) and optional restraints files (with *_restraints.txt suffix)"
+        },
+        "outdir": {
+            "type": "folder",
+            "description": "Directory for chai1 prediction results",
+            "default": "s3://omic/eureka/chai-lab/output",
+            "required": true,
+            "pipeline_io": "output",
+            "var_name": "params.outdir",
+            "examples": [
+                "s3://omic/eureka/chai-lab/output"
+            ],
+            "pattern": ".*",
+            "enum": [],
+            "validation": {},
+            "notes": "Directory where prediction results and log files will be stored. Will be created if it doesn't exist."
+        },
+        "use_msa": {
+            "type": "boolean",
+            "description": "Enable/disable MSA server usage",
+            "default": true,
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.use_msa",
+            "examples": [
+                true,
+                false
+            ],
+            "enum": [true, false],
+            "validation": {},
+            "notes": "Whether to use MSA server for improved predictions"
+        },
+        "msa_server": {
+            "type": "string",
+            "description": "MSA server URL",
+            "default": "https://api.colabfold.com",
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.msa_server",
+            "examples": [
+                "https://api.colabfold.com"
+            ],
+            "pattern": "^https?://.*",
+            "enum": [],
+            "validation": {},
+            "notes": "URL of the MSA server to use when use_msa is enabled"
+        },
+        "num_samples": {
+            "type": "integer",
+            "description": "Number of diffusion samples to generate",
+            "default": 5,
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.num_samples",
+            "examples": [
+                5,
+                10
+            ],
+            "pattern": "^[1-9]\\d*$",
+            "enum": [],
+            "validation": {
+                "min": 1,
+                "max": 50
+            },
+            "notes": "Number of structure samples to generate using diffusion"
+        }
+    }
+}