Add newlines and set command to fix #3416

CHANGELOG.md

@@ -13,6 +13,7 @@
 ### General
 
 - Fix `process.shell` in `nextflow.config` ([#3416](https://github.com/nf-core/tools/pull/3416))
+- Add newlines and set command to fix #3416 ([#3417](https://github.com/nf-core/tools/pull/3417))
 
 ## [v3.1.2 - Brass Boxfish Patch](https://github.com/nf-core/tools/releases/tag/3.1.2) - [2025-01-20]
 

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.