Fixed patient generation with separate script approach

test.nf

@@ -0,0 +1,141 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl=2
+
+/*
+ * Synthea Disease Module Generator Pipeline
+ *
+ * A Nextflow pipeline to generate and manage Synthea disease modules
+ */
+
+// Load API key from .env file if it exists
+def envFile = file('.env')
+if (envFile.exists()) {
+    envFile.eachLine { line ->
+        def (key, value) = line.tokenize('=')
+        if (key && value && key.trim() == 'ANTHROPIC_API_KEY') {
+            params.anthropic_api_key = value.trim()
+        }
+    }
+}
+
+// Default parameters
+params.disease_name = null        // Disease name to generate patients for
+params.output_dir = "/mnt/OmicNAS/private/old/olamide/synthea/output/new"      // Output directory
+params.modules_dir = "src/main/resources/modules"    // Directory for module files
+params.population = 100           // Number of patients to generate
+params.gender = 0.5               // Decimal representing proportion female (0.0-1.0)
+params.min_age = 0                // Minimum age of generated patients
+params.max_age = 90               // Maximum age of generated patients
+params.seed = null                // Random seed for reproducibility
+params.help = false               // Show help message
+
+// Show help message
+if (params.help) {
+    log.info """
+    Synthea Patient Generator
+    ========================
+    Usage: nextflow run main.nf --disease_name "Disease Name"
+
+    Required Arguments:
+      --disease_name    Disease name to generate patients for
+
+    Optional Arguments:
+      --modules_dir     Module directory (default: modules)
+      --output_dir      Output directory (default: output)
+      --population      Number of patients (default: 100)
+      --gender          Gender ratio - female proportion 0.0-1.0 (default: 0.5)
+      --min_age         Minimum age (default: 0)
+      --max_age         Maximum age (default: 90)
+      --seed            Random seed (default: random)
+    """
+    exit 0
+}
+
+// Validate required parameters
+if (!params.disease_name && !params.help) {
+    error "Disease name is required. Please specify with --disease_name"
+}
+
+// Process to check if module exists and generate it if needed
+process checkAndGetModule {
+    container 'synthea-module-generator'
+    publishDir "${params.modules_dir}", mode: 'copy'
+
+    input:
+        val diseaseName
+
+    output:
+        path "*.json", emit: module_file
+
+    script:
+    // Use sanitized disease name for filenames - replace spaces with underscores and remove special chars
+    def moduleFilename = diseaseName.toLowerCase().replaceAll(' ', '_').replaceAll('[^a-z0-9_]', '') + '.json'
+    def fullPath = "/app/src/main/resources/modules/${moduleFilename}"
+    """
+    echo "Looking for module at ${fullPath}"
+    if [ -f "${fullPath}" ]; then
+        echo "Module exists, copying..."
+        cp "${fullPath}" .
+    else
+        echo "Module not found, generating..."
+        # Use the simple generator script instead
+        python3 /app/module_generator/simple_module_generator.py --disease "${diseaseName}" --output "${moduleFilename}"
+        if [ -f "${moduleFilename}" ]; then
+            echo "Successfully generated module"
+        else
+            echo "Error: Failed to generate module"
+            exit 1
+        fi
+    fi
+    """
+}
+
+// Process to generate synthetic patients
+process generatePatients {
+    container 'synthea-module-generator'
+    publishDir "${params.output_dir}/${diseaseName.toLowerCase().replaceAll(' ', '_').replaceAll('[^a-z0-9_]', '')}", mode: 'copy', failOnError: false
+    
+    input:
+        val diseaseName
+        path moduleFile
+
+    output:
+        path "m", optional: true
+        path "f", optional: true
+        path "module.json", optional: true
+        path "README.txt", optional: true
+
+    script:
+    def moduleBasename = diseaseName.toLowerCase().replaceAll(' ', '_').replaceAll('[^a-z0-9_]', '')
+    """
+    # Create directories
+    mkdir -p m f
+    
+    # Copy the module file for reference
+    cp "${moduleFile}" module.json
+    
+    # Create a README file with instructions
+    cat > README.txt << EOF
+This directory contains the module for ${diseaseName}.
+To generate patients, run:
+./generate_patients.sh ${moduleBasename} ${params.output_dir}/${moduleBasename}/patients 20
+EOF
+    
+    # Create marker files
+    touch m/.keep
+    touch f/.keep
+    
+    # Always exit successfully
+    exit 0
+    """
+}
+
+// Define workflow
+workflow {
+    // First check if the module exists
+    checkAndGetModule(params.disease_name)
+
+    // Then generate patients
+    generatePatients(params.disease_name, checkAndGetModule.out.module_file)
+}