From 02d93f936007ac76dfce1b8fe504430eb8c548ba Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Wed, 25 Mar 2026 14:29:59 +0100
Subject: [PATCH] Fix image pull and gender arg for WES

- Push as Docker V2 manifest (no OCI index/attestation) so K8s can pull
- Tag as v3 to avoid cached image issues
- Fix gender: omit -g flag for 0.5 (both), Synthea only accepts M or F
---
 main.nf         | 6 +++---
 nextflow.config | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/main.nf b/main.nf
index c293112..696efae 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:v2'
+    container 'harbor.cluster.omic.ai/omic/synthea-alldiseases:v3'
     publishDir params.outdir, mode: 'copy'
 
     input:
@@ -34,13 +34,13 @@ process generatePatients {
 
     script:
     def moduleBasename = diseaseName.toLowerCase().replaceAll(' ', '_')
-    def genderArg = params.gender < 0.5 ? "M" : (params.gender > 0.5 ? "F" : "B")
+    def genderArg = params.gender < 0.5 ? "-g M" : (params.gender > 0.5 ? "-g F" : "")
     def seedArg = params.seed ? "-s ${params.seed}" : ""
     """
     # 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} \
+        ${genderArg} \
         -a ${params.min_age}-${params.max_age} \
         ${seedArg} 2>&1 | tee run.log
 
diff --git a/nextflow.config b/nextflow.config
index ab5b9b8..bf4e64c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -26,7 +26,7 @@ profiles {
     k8s {
         process {
             executor = 'k8s'
-            container = 'harbor.cluster.omic.ai/omic/synthea-alldiseases:v2'
+            container = 'harbor.cluster.omic.ai/omic/synthea-alldiseases:v3'
         }
         docker {
             enabled = true