Refactor to capture exit_status for successful runs

The submission script would incorrectly report a workflow error even
when it finished successfully. This was due to the inline exit_status
assignment logic, which only captured unsuccessful runs, leaving the
exit_status variable unassigned for successful runs. This resulted in an
"unbound variable" error message in the logs. To address this issue, we
moved the exit_status assignment to the next line (not inline) to ensure
that the variable is properly assigned even for successful runs
(exit code 0) of the snakemake command. This change resolves the issue
and ensures accurate reporting of workflow status.

Fixes #262

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