Fix script to write outputs to Nextflow work dir

- Save pwd before cd /app so outputs go to correct location
- Use set +e and PIPESTATUS to handle java exit code gracefully
- Exit 0 if FHIR files were generated successfully

main.nf

@@ -37,20 +37,34 @@ process generatePatients {
     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)
-    cd /app && java -jar /app/build/libs/synthea-with-dependencies.jar \
+    cd /app
+    java -jar /app/build/libs/synthea-with-dependencies.jar \
         -p ${params.population} \
         ${genderArg} \
         -a ${params.min_age}-${params.max_age} \
-        ${seedArg} 2>&1 | tee run.log
+        ${seedArg} 2>&1 | tee \${WORKDIR}/run.log
+    JAVA_EXIT=\${PIPESTATUS[0]}
 
-    # Collect FHIR output
+    # 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
-        echo "Copied \$(ls fhir/*.json 2>/dev/null | wc -l) FHIR bundles" | tee -a run.log
+        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 generated" | tee -a run.log
+        echo "Warning: No FHIR output directory found" | tee -a run.log
+    fi
+
+    # Exit 0 if we got FHIR output, regardless of java exit code
+    if [ -n "\$(ls fhir/*.json 2>/dev/null)" ]; then
+        exit 0
+    else
+        exit \${JAVA_EXIT}
     fi
     """
 }