From 326ecfb3ee1b27f134fdec4d99da05dd32281ab7 Mon Sep 17 00:00:00 2001
From: Eric <eb167@nyu.edu>
Date: Wed, 24 Jan 2024 21:20:28 -0500
Subject: [PATCH 1/2] Create cluster.config

---
 cluster.config | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 cluster.config

diff --git a/cluster.config b/cluster.config
new file mode 100644
index 0000000..6ec18fc
--- /dev/null
+++ b/cluster.config
@@ -0,0 +1,23 @@
+// Configuration settings for NYU Greene HPC Cluster
+
+params {
+  max_memory = 3000.GB
+  max_cpus = 96
+  max_time = 7.d
+}
+
+singularity.enabled = true
+
+process {
+  executor = 'slurm'
+  clusterOptions = '--export=NONE'
+  scratch = true
+  maxRetries = 3
+  errorStrategy = { task.attempt <=3 ? 'retry' : 'finish' }
+  cache = 'lenient'
+}
+
+executor {
+  queueSize = 1900
+  submitRateLimit = '20 sec'
+}

From 8d3a377be3e4c21e69138a16ca4d1ffb3c83af95 Mon Sep 17 00:00:00 2001
From: Eric <eb167@nyu.edu>
Date: Wed, 24 Jan 2024 21:23:24 -0500
Subject: [PATCH 2/2] Add cluster.config

---
 launch.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/launch.sh b/launch.sh
index 0d171ea..9f39f18 100644
--- a/launch.sh
+++ b/launch.sh
@@ -19,6 +19,7 @@ log_dir="/scratch/gencore/GENEFLOW/alpha/logs/${fcid}/pipeline"
 
 nextflow_command="nextflow \
   -log ${log_dir}/nextflow.log run /home/gencore/SCRIPTS/GENEFLOW/main.nf \
+  -c /home/gencore/SCRIPTS/GENEFLOW/cluster.config \
   -c /home/gencore/SCRIPTS/GENEFLOW/nextflow.config \
   --run_dir_path $run_dir_path \
   --trace_file_path ${log_dir}/trace.txt \