diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 217b1c254..de6e0fac9 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -240,10 +240,10 @@ env {
 // Set bash options
 process.shell = [
     "bash",
-    "-C",         // No clobber - prevent output redirection from overwriting files.
-    "-e",         // Exit if a tool returns a non-zero status/exit code
-    "-u",         // Treat unset variables and parameters as an error
-    "-o pipefail" // Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
+    "\nset -C",         // No clobber - prevent output redirection from overwriting files.
+    "\nset -e",         // Exit if a tool returns a non-zero status/exit code
+    "\nset -u",         // Treat unset variables and parameters as an error
+    "\nset -o pipefail" // Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
 ]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.