Trying to fix basic functionality again.

nextflow.config

@@ -0,0 +1,51 @@
+// Nextflow configuration file
+manifest {
+  description = 'Synthea Module Generator Pipeline'
+}
+
+// Load parameters from params.json
+def paramsJson = new File("$baseDir/params.json").text
+def paramsData = new groovy.json.JsonSlurper().parseText(paramsJson)
+
+// Merge with defaults
+params {
+  disease_name = paramsData.disease_name
+  modules_dir = paramsData.modules_dir ?: "/Users/richman/workspace/synthea-alldiseases/modules"
+  output_dir = paramsData.output_dir ?: "output"
+  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 $baseDir/.env:/app/.env"
+}
+
+process {
+  container = 'synthea-module-generator'
+  containerOptions = "-e MODULES_DIR=/app/src/main/resources/modules -e PYTHONPATH=/app -e ANTHROPIC_API_KEY=${params.anthropic_api_key}"
+}
+
+trace {
+  enabled = true
+  overwrite = true
+  file = "$baseDir/trace.txt"
+}
+
+profiles {
+  standard {
+    process.executor = 'local'
+  }
+}