fix: prevent unbound var error on irods acc

RIVM-bioinformatics · Sep 5, 2024 · 9c89b0f · 9c89b0f
1 parent 9b28031
commit 9c89b0f
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/run_pipeline.sh b/run_pipeline.sh
@@ -17,11 +17,13 @@ else
     exit 1
 fi
 
+set +u
 #check if there is an exclusion file, if so change the parameter
 if [ ! -z "${irods_input_sequencing__run_id}" ] && [ -f "/data/BioGrid/NGSlab/sample_sheets/${irods_input_sequencing__run_id}.exclude" ]
 then
   EXCLUSION_FILE="/data/BioGrid/NGSlab/sample_sheets/${irods_input_sequencing__run_id}.exclude"
 fi
+set -u
 
 if [ ! -d "${input_dir}" ] || [ ! -d "${output_dir}" ]
 then