From 72b0cebdbeeb74515b1262cee6962369ccb68966 Mon Sep 17 00:00:00 2001
From: Jorisvansteenbrugge
 <7196110+Jorisvansteenbrugge@users.noreply.github.com>
Date: Wed, 13 May 2026 11:30:06 +0200
Subject: [PATCH 1/2] increases resources main job and tmpspace umitools dedup

---
 conf/modules.config | 3 ++-
 run_nextflow_rna.sh | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index cfac987..31c4a73 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -295,7 +295,8 @@ process {
     }
 
     withName: UMITOOLS_DEDUP {
-        clusterOptions = "${params.cluster_options} --gres=tmpspace:40G"
+        cache          = false // Never resume this process to avoid downstream errors
+        clusterOptions = "${params.cluster_options} --gres=tmpspace:200G"
         ext.args       = {
             [
                 "--umi-separator=:",
diff --git a/run_nextflow_rna.sh b/run_nextflow_rna.sh
index d3caaa2..d5837b1 100755
--- a/run_nextflow_rna.sh
+++ b/run_nextflow_rna.sh
@@ -50,7 +50,7 @@ fi
 
 sbatch <<EOT
 #!/bin/bash
-#SBATCH --time=24:00:00
+#SBATCH --time=48:00:00
 #SBATCH --nodes=1
 #SBATCH --mem 10G
 #SBATCH --gres=tmpspace:10G

From 72257d8a81738b6193df1beeccc0a6cf19175520 Mon Sep 17 00:00:00 2001
From: Joris van Steenbrugge <Jorisvansteenbrugge@users.noreply.github.com>
Date: Wed, 13 May 2026 14:10:16 +0200
Subject: [PATCH 2/2] fix syntax error

---
 conf/modules.config | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index e9ba2d6..21be643 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -385,11 +385,7 @@ process {
 
     withName: UMITOOLS_DEDUP {
         cache          = false // Never resume this process to avoid downstream errors
-<<<<<<< hotfix/v1.1.3
         clusterOptions = "${params.cluster_options} --gres=tmpspace:200G"
-=======
-        clusterOptions = "${params.cluster_options} --gres=tmpspace:40G"
->>>>>>> develop
         ext.args       = {
             [
                 "--umi-separator=:",