From f29323323b4d45c9378c2fcc445bc0c1d7c230e3 Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Wed, 25 Mar 2026 13:30:24 +0100
Subject: [PATCH] Use pre-built jar and v2 tag to bypass Gradle permission
 issue

- Call java -jar synthea-with-dependencies.jar directly instead of
  run_synthea which invokes Gradle at runtime
- Tag image as v2 to force K8s to pull fresh image
---
 main.nf         | 17 ++++-------------
 nextflow.config |  2 +-
 2 files changed, 5 insertions(+), 14 deletions(-)

diff --git a/main.nf b/main.nf
index 7eebb8a..c293112 100644
--- a/main.nf
+++ b/main.nf
@@ -22,7 +22,7 @@ if (!params.outdir) {
 
 // Process to generate synthetic patients
 process generatePatients {
-    container 'harbor.cluster.omic.ai/omic/synthea-alldiseases:latest'
+    container 'harbor.cluster.omic.ai/omic/synthea-alldiseases:v2'
     publishDir params.outdir, mode: 'copy'
 
     input:
@@ -37,21 +37,12 @@ process generatePatients {
     def genderArg = params.gender < 0.5 ? "M" : (params.gender > 0.5 ? "F" : "B")
     def seedArg = params.seed ? "-s ${params.seed}" : ""
     """
-    # Check if a custom module exists, otherwise use built-in Synthea modules
-    MODULE_FILE="/app/src/main/resources/modules/${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 \
+    # Use pre-built jar directly (bypasses Gradle which needs write access to .gradle)
+    cd /app && java -jar /app/build/libs/synthea-with-dependencies.jar \
         -p ${params.population} \
         -g ${genderArg} \
         -a ${params.min_age}-${params.max_age} \
-        ${seedArg} \
-        -- ${diseaseName} 2>&1 | tee -a run.log
+        ${seedArg} 2>&1 | tee run.log
 
     # Collect FHIR output
     mkdir -p fhir
diff --git a/nextflow.config b/nextflow.config
index 9dd640b..ab5b9b8 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -26,7 +26,7 @@ profiles {
     k8s {
         process {
             executor = 'k8s'
-            container = 'harbor.cluster.omic.ai/omic/synthea-alldiseases:latest'
+            container = 'harbor.cluster.omic.ai/omic/synthea-alldiseases:v2'
         }
         docker {
             enabled = true