From 4cd23d549b23e745a4ef63f62b58c35f6084516b Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Thu, 26 Mar 2026 17:46:41 +0100
Subject: [PATCH] Fix HOME env for colabfold weight download, increase
 resources, use v3 tag

---
 Dockerfile.wes  | 4 ++++
 main.nf         | 6 +++---
 nextflow.config | 7 ++++---
 3 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/Dockerfile.wes b/Dockerfile.wes
index 84f40a2..a0e8fbb 100644
--- a/Dockerfile.wes
+++ b/Dockerfile.wes
@@ -14,6 +14,10 @@ RUN python3 -m pip install --upgrade pip && \
 # Add user entry for UID 1000 (k8s default) to avoid getpwuid errors
 RUN useradd -u 1000 -m -s /bin/bash nextflow || true
 
+# Set HOME for UID 1000 so colabfold weights download to writable location
+ENV HOME=/home/nextflow
+RUN mkdir -p /home/nextflow/.cache && chmod -R 777 /home/nextflow
+
 RUN mkdir -p /opt/bioemu/scripts/ /data /results && chmod -R 777 /data /results
 
 COPY calculate_gibbs.py /opt/bioemu/scripts/
diff --git a/main.nf b/main.nf
index df62821..1ddc415 100644
--- a/main.nf
+++ b/main.nf
@@ -13,7 +13,7 @@ params.temperature = 300
 params.n_clusters = 5
 
 process GENERATE_STRUCTURE_1 {
-    container 'harbor.cluster.omic.ai/omic/bioemu:v2'
+    container 'harbor.cluster.omic.ai/omic/bioemu:v3'
     publishDir "${params.outdir}/${params.complex_name}/protein1", mode: 'copy'
 
     input:
@@ -41,7 +41,7 @@ process GENERATE_STRUCTURE_1 {
 }
 
 process GENERATE_STRUCTURE_2 {
-    container 'harbor.cluster.omic.ai/omic/bioemu:v2'
+    container 'harbor.cluster.omic.ai/omic/bioemu:v3'
     publishDir "${params.outdir}/${params.complex_name}/protein2", mode: 'copy'
 
     input:
@@ -69,7 +69,7 @@ process GENERATE_STRUCTURE_2 {
 }
 
 process CALCULATE_BINDING {
-    container 'harbor.cluster.omic.ai/omic/bioemu:v2'
+    container 'harbor.cluster.omic.ai/omic/bioemu:v3'
     publishDir "${params.outdir}/${params.complex_name}/analysis", mode: 'copy'
 
     input:
diff --git a/nextflow.config b/nextflow.config
index 6bc3874..c35632c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -11,9 +11,10 @@ docker {
 }
 
 process {
-    container = 'harbor.cluster.omic.ai/omic/bioemu:v2'
-    cpus = 2
-    memory = '8 GB'
+    container = 'harbor.cluster.omic.ai/omic/bioemu:v3'
+    cpus = 4
+    memory = '16 GB'
+    time = '2h'
 }
 
 profiles {