From 5f4711aef970c9f879bdafb39ab863b3c95a0595 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karatu=C4=9F=20Ozan=20Bircan?= <karatugo@ebi.ac.uk>
Date: Fri, 1 Dec 2023 10:23:56 +0300
Subject: [PATCH 1/2] feat: Migrate from LSF to SLURM

This commit changes the job scheduler in the project's configuration and wrapper script from LSF to SLURM.
---
 example_wrapper.sh | 2 +-
 nextflow.config    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/example_wrapper.sh b/example_wrapper.sh
index 4774c80b..d90b8da5 100644
--- a/example_wrapper.sh
+++ b/example_wrapper.sh
@@ -13,4 +13,4 @@ mkdir -p $folder
 
 cd $folder
 nextflow $nextflow -c $config --inputPath $folder --to_harm_folder $to_harm -resume 
-#further function: --execute local(or LSF)
+#further function: --execute local (or SLURM)
diff --git a/nextflow.config b/nextflow.config
index 6f957cba..f9a00fd0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -87,7 +87,7 @@ profiles {
         process.executor = 'local'
     }
     cluster {
-        process.executor = 'lsf'
+        process.executor = 'slurm'
         process.queue = 'short'
         process.memory = '28GB'
     }

From 4cbb8b9e5be9e2a02db1767086f0cbc26a7ada46 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Karatu=C4=9F=20Ozan=20Bircan?= <karatugo@ebi.ac.uk>
Date: Fri, 1 Dec 2023 15:26:32 +0300
Subject: [PATCH 2/2] feat: Add execution time limit in SLURM profile

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index f9a00fd0..efcb553c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -88,8 +88,8 @@ profiles {
     }
     cluster {
         process.executor = 'slurm'
-        process.queue = 'short'
         process.memory = '28GB'
+        process.time = '2d'
     }
     conda {
         params.enable_conda    = true