Clean up pipeline files

- Remove unused variable and redundant comments/echo statements in main.nf
- Remove obsolete files: simple.nf, test.nf, generate_patients.sh,
  test_synthea.sh, trace.txt, docker-compose.yml
  (all referenced local-only synthea-module-generator image)

main.nf

@@ -2,7 +2,6 @@
 
 nextflow.enable.dsl=2
 
-// Default parameters
 params.disease_name = null
 params.outdir = null
 params.population = 10
@@ -11,7 +10,6 @@ params.min_age = 0
 params.max_age = 90
 params.seed = null
 
-// Validate required parameters
 if (!params.disease_name) {
     error "Disease name is required. Please specify with --disease_name"
 }
@@ -20,7 +18,6 @@ if (!params.outdir) {
     error "Output directory is required. Please specify with --outdir"
 }
 
-// Process to generate synthetic patients
 process generatePatients {
     container 'harbor.cluster.omic.ai/omic/synthea-alldiseases:v3'
     publishDir params.outdir, mode: 'copy'
@@ -33,14 +30,13 @@ process generatePatients {
         path "run.log", emit: log_file
 
     script:
-    def moduleBasename = diseaseName.toLowerCase().replaceAll(' ', '_')
     def genderArg = params.gender < 0.5 ? "-g M" : (params.gender > 0.5 ? "-g F" : "")
     def seedArg = params.seed ? "-s ${params.seed}" : ""
     """
     set +e
     WORKDIR=\$(pwd)
 
-    # Use pre-built jar directly (bypasses Gradle which needs write access to .gradle)
+    # Run Synthea via pre-built jar (Gradle is not writable in K8s)
     cd /app
     java -jar /app/build/libs/synthea-with-dependencies.jar \
         -p ${params.population} \
@@ -49,18 +45,13 @@ process generatePatients {
         ${seedArg} 2>&1 | tee \${WORKDIR}/run.log
     JAVA_EXIT=\${PIPESTATUS[0]}
 
-    # Collect FHIR output back into Nextflow work dir
     cd \${WORKDIR}
     mkdir -p fhir
     if [ -d /app/output/fhir ]; then
         cp /app/output/fhir/*.json fhir/ 2>/dev/null || true
-        FHIR_COUNT=\$(ls fhir/*.json 2>/dev/null | wc -l)
-        echo "Copied \${FHIR_COUNT} FHIR bundles" | tee -a run.log
-    else
-        echo "Warning: No FHIR output directory found" | tee -a run.log
     fi
 
-    # Exit 0 if we got FHIR output, regardless of java exit code
+    # Succeed if FHIR output was produced
     if [ -n "\$(ls fhir/*.json 2>/dev/null)" ]; then
         exit 0
     else
@@ -69,7 +60,6 @@ process generatePatients {
     """
 }
 
-// Workflow
 workflow {
     generatePatients(params.disease_name)
 }