Merge pull request #272 from NCI-CGR/issue-262

Refactor to capture exit_status for successful runs
NCI-CGR · Apr 12, 2024 · 45f2764 · 45f2764
2 parents 458b6bb + 809c14f
commit 45f2764
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/src/cgr_gwas_qc/cluster_profiles/snakemake.sh b/src/cgr_gwas_qc/cluster_profiles/snakemake.sh
@@ -191,7 +191,8 @@ run_workflow() {
   {{ python_executable }} -m cgr_gwas_qc snakemake \
     --local-cores {{ local_tasks }} \
     --profile {{ profile }} \
-    {{ added_options }} || exit_status=$?  # Don't exit on failure, see why we exited
+    {{ added_options }}
+  exit_status=$?
 
   if (( exit_status != 0 )) && log_says_locked; then
     exit 42