Configure synthea-alldiseases for WES execution

- Rewrite params.json to match WES tool registry format
- Update main.nf to use Harbor container image
- Add k8s profile to nextflow.config for WES/Kubernetes execution
- Use s3://omic/eureka paths for output

main.nf

@@ -2,127 +2,69 @@
 
 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
-}
+params.disease_name = null
+params.outdir = null
+params.population = 10
+params.gender = 0.5
+params.min_age = 0
+params.max_age = 90
+params.seed = null
 
 // Validate required parameters
-if (!params.disease_name && !params.help) {
+if (!params.disease_name) {
     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
-    """
+if (!params.outdir) {
+    error "Output directory is required. Please specify with --outdir"
 }
 
 // Process to generate synthetic patients
 process generatePatients {
-    container 'synthea-module-generator'
-    publishDir "${params.output_dir}/${diseaseName.toLowerCase().replaceAll(' ', '_')}", mode: 'copy'
-    
+    container 'harbor.cluster.omic.ai/omic/synthea-alldiseases:latest'
+    publishDir params.outdir, mode: 'copy'
+
     input:
         val diseaseName
-        path moduleFile
-    
+
     output:
-        path "m/*", optional: true
-        path "f/*", optional: true
-    
+        path "fhir/*.json", optional: true, emit: fhir_output
+        path "run.log", emit: log_file
+
     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)
+    def seedArg = params.seed ? "-s ${params.seed}" : ""
     """
-    # Copy module and run Synthea
-    cp "${moduleFile}" /app/modules/
-    cd /app && ./run_synthea -p ${params.population} -g ${genderArg} -m ${moduleBasename} -a ${params.min_age}-${params.max_age} -s ${seedValue}
-    
-    # Organize output by gender
-    mkdir -p m f
-    find /app/output/fhir -type f -name "*.json" ! -name "*hospital*" ! -name "*practitioner*" | xargs grep -l '"gender":"male"' | xargs -I{} cp {} m/
-    find /app/output/fhir -type f -name "*.json" ! -name "*hospital*" ! -name "*practitioner*" | xargs grep -l '"gender":"female"' | xargs -I{} cp {} f/
+    # Check if a custom module exists, otherwise use built-in Synthea modules
+    MODULE_FILE="/app/src/main/resources/modules/${moduleBasename}.json"
+    if [ -f "\${MODULE_FILE}" ]; then
+        echo "Found custom module: \${MODULE_FILE}" | tee run.log
+    else
+        echo "Using built-in Synthea modules for: ${diseaseName}" | tee run.log
+    fi
+
+    # Run Synthea patient generation
+    cd /app && ./run_synthea \
+        -p ${params.population} \
+        -g ${genderArg} \
+        -a ${params.min_age}-${params.max_age} \
+        ${seedArg} \
+        -- ${diseaseName} 2>&1 | tee -a run.log
+
+    # Collect FHIR output
+    mkdir -p fhir
+    if [ -d /app/output/fhir ]; then
+        cp /app/output/fhir/*.json fhir/ 2>/dev/null || true
+        echo "Copied \$(ls fhir/*.json 2>/dev/null | wc -l) FHIR bundles" | tee -a run.log
+    else
+        echo "Warning: No FHIR output generated" | tee -a run.log
+    fi
     """
 }
 
-// Define workflow
+// Workflow
 workflow {
-    // First check if the module exists
-    checkAndGetModule(params.disease_name)
-    
-    // Then generate patients
-    generatePatients(params.disease_name, checkAndGetModule.out.module_file)
+    generatePatients(params.disease_name)
 }