Trying to fix basic functionality again.

main.nf

@@ -0,0 +1,128 @@
+#!/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 = "output"      // 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 "${params.modules_dir}", mode: 'copy'
+    
+    input:
+        val diseaseName
+    
+    output:
+        path "*.json", emit: module_file
+    
+    script:
+    def moduleFilename = diseaseName.toLowerCase().replaceAll(' ', '_') + '.json'
+    def fullPath = "/app/src/main/resources/modules/${moduleFilename}"
+    """
+    echo "Looking for module at ${fullPath}"
+    if [ -f "${fullPath}" ]; then
+        echo "Module exists, copying..."
+        cp "${fullPath}" .
+    else
+        echo "Module not found, generating..."
+        python3 /app/module_generator/module_generator.py --disease "${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(' ', '_')}", mode: 'copy'
+    
+    input:
+        val diseaseName
+        path moduleFile
+    
+    output:
+        path "m/*", optional: true
+        path "f/*", optional: true
+    
+    script:
+    def moduleBasename = diseaseName.toLowerCase().replaceAll(' ', '_')
+    def genderArg = params.gender < 0.5 ? "M" : (params.gender > 0.5 ? "F" : "B")
+    def seedValue = params.seed ?: new Random().nextInt(1000000)
+    """
+    # Copy module and run Synthea
+    cp "${moduleFile}" /app/modules/
+    cd /app && ./run_synthea -p ${params.population} -g ${genderArg} -m ${moduleBasename} -a ${params.min_age}-${params.max_age} -s ${seedValue}
+    
+    # Organize output by gender
+    mkdir -p m f
+    find /app/output/fhir -type f -name "*.json" ! -name "*hospital*" ! -name "*practitioner*" | xargs grep -l '"gender":"male"' | xargs -I{} cp {} m/
+    find /app/output/fhir -type f -name "*.json" ! -name "*hospital*" ! -name "*practitioner*" | xargs grep -l '"gender":"female"' | xargs -I{} cp {} f/
+    """
+}
+
+// Define workflow
+workflow {
+    // First check if the module exists
+    checkAndGetModule(params.disease_name)
+    
+    // Then generate patients
+    generatePatients(params.disease_name, checkAndGetModule.out.module_file)
+}