Trying to fix basic functionality again.

simple.nf

@@ -0,0 +1,77 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl=2
+
+// Default parameters
+params.disease_name = "Diabetes"  // Default disease name
+params.output_dir = "output"      // Output directory
+params.modules_dir = "modules"    // Directory for module files
+
+// Process to generate synthetic patients
+process generatePatients {
+    publishDir "${params.output_dir}/${params.disease_name.toLowerCase().replaceAll(' ', '_')}", mode: 'copy'
+    
+    input:
+    path moduleFile
+    
+    output:
+    path "**"
+    
+    script:
+    """
+    echo "Module file: ${moduleFile}"
+    echo "Disease: ${params.disease_name}"
+    
+    # Check if Docker is available
+    if command -v docker &>/dev/null; then
+        echo "Docker is available, looking for Synthea container..."
+        
+        # Find the Synthea container
+        container_id=\$(docker ps --format '{{.ID}}' --filter "name=synthea" | head -1)
+        
+        if [ -n "\$container_id" ]; then
+            echo "Using Synthea container \$container_id"
+            
+            # Copy module to container
+            docker exec \$container_id mkdir -p /app/modules
+            docker cp "${moduleFile}" \$container_id:/app/modules/
+            
+            # Run Synthea with minimal parameters
+            docker exec \$container_id bash -c "cd /app && ./run_synthea -p 1 -m ${params.disease_name.toLowerCase().replaceAll(' ', '_')}"
+            
+            # Copy output from container
+            docker cp \$container_id:/app/output/fhir ./ || mkdir -p ./fhir
+            docker cp \$container_id:/app/output/metadata ./ || mkdir -p ./metadata
+            
+            echo "Completed patient generation"
+        else
+            echo "No Synthea container found, creating mock output for testing"
+            mkdir -p ./fhir ./metadata
+            echo "Mock FHIR data for ${params.disease_name}" > ./fhir/mock_patient.json
+            echo "Mock metadata for ${params.disease_name}" > ./metadata/mock_stats.json
+        fi
+    else
+        echo "Docker not available, creating mock output for testing"
+        mkdir -p ./fhir ./metadata
+        echo "Mock FHIR data for ${params.disease_name}" > ./fhir/mock_patient.json
+        echo "Mock metadata for ${params.disease_name}" > ./metadata/mock_stats.json
+    fi
+    """
+}
+
+// Define workflow
+workflow {
+    // Prepare module file
+    moduleFilename = params.disease_name.toLowerCase().replaceAll(' ', '_') + '.json'
+    moduleFile = file("${params.modules_dir}/${moduleFilename}")
+    
+    if (!moduleFile.exists()) {
+        error "Module file not found: ${moduleFile}"
+    }
+    
+    // Create a channel with the module file
+    moduleChannel = Channel.fromPath(moduleFile)
+    
+    // Generate patients
+    generatePatients(moduleChannel)
+}