From df0d68f1399767f74bfcf55ca74dcb897b97b52e Mon Sep 17 00:00:00 2001
From: boasvdp <boasvdp@gmail.com>
Date: Fri, 6 Sep 2024 09:49:12 +0200
Subject: [PATCH] chore: set time limit to 600 for GATK

---
 run_pipeline.sh | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/run_pipeline.sh b/run_pipeline.sh
index 8d48439..355b0a0 100755
--- a/run_pipeline.sh
+++ b/run_pipeline.sh
@@ -92,6 +92,7 @@ fi
 export SINGULARITY_TMPDIR="$(pwd)"
 
 #without exclusion file
+# set time limit to 600 minutes in case large files are present. GATK is slow.
 if [ "${EXCLUSION_FILE}" == "" ]
 then
     python juno_mapping.py \
@@ -99,7 +100,8 @@ then
         -i "${input_dir}" \
         -o "${output_dir}" \
         -s "${SPECIES}" \
-        --prefix "/mnt/db/juno/sing_containers"
+        --prefix "/mnt/db/juno/sing_containers" \
+        -tl 600
 
         result=$?
 else
@@ -109,7 +111,8 @@ else
         -o "${output_dir}" \
         -s "${SPECIES}" \
         --prefix "/mnt/db/juno/sing_containers" \
-        -ex "${EXCLUSION_FILE}"
+        -ex "${EXCLUSION_FILE}" \
+        -tl 600
 
         result=$?
 fi