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

nextflow.config

@@ -1,54 +1,44 @@
-// Nextflow configuration file
 manifest {
-  description = 'Synthea Module Generator Pipeline'
+    name = 'synthea-alldiseases'
+    description = 'Synthea synthetic patient generator pipeline'
+    mainScript = 'main.nf'
+    version = '1.0.0'
 }
 
-// Load parameters from params.json
-def paramsJson = new File("$baseDir/params.json").text
-def paramsData = new groovy.json.JsonSlurper().parseText(paramsJson)
-
-// Keep work directories for debugging
-cleanup = false
-
-// Merge with defaults
 params {
-  local_output_dir = "$baseDir/local_output"
-  disease_name = paramsData.disease_name
-  modules_dir = paramsData.modules_dir ?: "/Users/richman/workspace/synthea-alldiseases/modules"
-  output_dir = paramsData.output_dir ?: "/mnt/OmicNAS/private/old/olamide/synthea/output/new" 
-  population = paramsData.population ?: 100
-  gender = paramsData.gender ?: 0.5
-  min_age = paramsData.min_age ?: 0
-  max_age = paramsData.max_age ?: 90
-  seed = paramsData.seed
-  generate_patients = paramsData.generate_patients ?: true
-  publish_dir = paramsData.publish_dir ?: "published_output"
-  // Additional params
-  max_cost = 5.0
-  timeout = 300
-  anthropic_api_key = null
-  batch_size = 1
-  help = false
-}
-
-docker {
-  enabled = true
-  runOptions = "-v $baseDir/$params.modules_dir:/app/src/main/resources/modules -v $baseDir/src/main/python:/app/src/main/python -v $baseDir/src/main/resources:/app/src/main/resources -v $baseDir/.env:/app/.env -v $baseDir/module_generator:/app/module_generator -v $baseDir/modules:/app/modules"
-}
-
-process {
-  container = 'synthea-module-generator'
-  containerOptions = "-e MODULES_DIR=/app/src/main/resources/modules -e PYTHONPATH=/app -e ANTHROPIC_API_KEY=${params.anthropic_api_key}"
-}
-
-trace {
-  enabled = true
-  overwrite = true
-  file = "$baseDir/trace.txt"
+    disease_name = null
+    outdir = null
+    population = 10
+    gender = 0.5
+    min_age = 0
+    max_age = 90
+    seed = null
 }
 
 profiles {
-  standard {
-    process.executor = 'local'
-  }
+    standard {
+        docker {
+            enabled = true
+            temp = 'auto'
+        }
+    }
+
+    k8s {
+        process {
+            executor = 'k8s'
+            container = 'harbor.cluster.omic.ai/omic/synthea-alldiseases:latest'
+        }
+        docker {
+            enabled = true
+        }
+        k8s {
+            storageClaimName = 'eureka-pvc'
+            storageMountPath = '/omic/eureka'
+        }
+    }
+}
+
+process {
+    cpus = 2
+    memory = '4 GB'
 }