Fixed patient generation with separate script approach

nextflow.config

@@ -7,11 +7,15 @@ manifest {
 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 ?: "output"
+  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
@@ -19,7 +23,6 @@ params {
   seed = paramsData.seed
   generate_patients = paramsData.generate_patients ?: true
   publish_dir = paramsData.publish_dir ?: "published_output"
-  
   // Additional params
   max_cost = 5.0
   timeout = 300
@@ -30,7 +33,7 @@ params {
 
 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"
+  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 {