chore: set time limit to 600 for GATK

RIVM-bioinformatics · Sep 6, 2024 · df0d68f · df0d68f
1 parent 9c89b0f
commit df0d68f
Showing 1 changed file with 5 additions and 2 deletions.
diff --git a/run_pipeline.sh b/run_pipeline.sh
@@ -92,14 +92,16 @@ fi
 export SINGULARITY_TMPDIR="$(pwd)"
 
 #without exclusion file
+# set time limit to 600 minutes in case large files are present. GATK is slow.
 if [ "${EXCLUSION_FILE}" == "" ]
 then
     python juno_mapping.py \
         --queue "${QUEUE}" \
         -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