Configure synthea-alldiseases for WES execution

- Rewrite params.json to match WES tool registry format
- Update main.nf to use Harbor container image
- Add k8s profile to nextflow.config for WES/Kubernetes execution
- Use s3://omic/eureka paths for output

params.json

@@ -1,14 +1,117 @@
 {
-  "disease_name": "Parkinson's Disease",
-  "modules_dir": "modules",
-  "output_dir": "/mnt/OmicNAS/private/old/olamide/synthea/output/new",
-  "generate_patients": true,
-  "population": 10,
-  "gender": 0.5,
-  "min_age": 0,
-  "max_age": 90,
-  "analyze_patient_data": false,
-  "report_format": "html",
-  "force_generate": false,
-  "publish_dir": "published_output"
+    "params": {
+        "disease_name": {
+            "type": "string",
+            "description": "Disease name to generate synthetic patients for",
+            "default": "Diabetes",
+            "required": true,
+            "pipeline_io": "parameter",
+            "var_name": "params.disease_name",
+            "examples": [
+                "Diabetes",
+                "Hypertension",
+                "Lung Cancer"
+            ],
+            "pattern": ".*",
+            "enum": [],
+            "validation": {},
+            "notes": "The disease name used to find or generate a Synthea disease module. Case-insensitive."
+        },
+        "population": {
+            "type": "integer",
+            "description": "Number of synthetic patients to generate",
+            "default": 10,
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.population",
+            "examples": [
+                10,
+                100,
+                1000
+            ],
+            "pattern": "^\\d+$",
+            "enum": [],
+            "validation": {
+                "min": 1,
+                "max": 10000
+            },
+            "notes": "Higher numbers take longer to generate."
+        },
+        "gender": {
+            "type": "number",
+            "description": "Proportion of female patients (0.0 = all male, 1.0 = all female)",
+            "default": 0.5,
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.gender",
+            "examples": [
+                0.5,
+                0.0,
+                1.0
+            ],
+            "pattern": "^[01]\\.?\\d*$",
+            "enum": [],
+            "validation": {
+                "min": 0.0,
+                "max": 1.0
+            },
+            "notes": "Decimal between 0.0 and 1.0 representing the proportion of female patients."
+        },
+        "min_age": {
+            "type": "integer",
+            "description": "Minimum age of generated patients",
+            "default": 0,
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.min_age",
+            "examples": [
+                0,
+                18,
+                40
+            ],
+            "pattern": "^\\d+$",
+            "enum": [],
+            "validation": {
+                "min": 0,
+                "max": 140
+            },
+            "notes": "Minimum patient age in years."
+        },
+        "max_age": {
+            "type": "integer",
+            "description": "Maximum age of generated patients",
+            "default": 90,
+            "required": false,
+            "pipeline_io": "parameter",
+            "var_name": "params.max_age",
+            "examples": [
+                90,
+                65,
+                100
+            ],
+            "pattern": "^\\d+$",
+            "enum": [],
+            "validation": {
+                "min": 1,
+                "max": 140
+            },
+            "notes": "Maximum patient age in years."
+        },
+        "outdir": {
+            "type": "folder",
+            "description": "Output directory for generated patient data",
+            "default": "s3://omic/eureka/synthea-alldiseases/output",
+            "required": true,
+            "pipeline_io": "output",
+            "var_name": "params.outdir",
+            "examples": [
+                "s3://omic/eureka/synthea-alldiseases/output",
+                "s3://omic/eureka/synthea-alldiseases/results"
+            ],
+            "pattern": ".*",
+            "enum": [],
+            "validation": {},
+            "notes": "Directory where generated FHIR patient bundles will be stored."
+        }
+    }
 }