// 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'
  }
}