diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3e2c722..2f8b615 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,7 +8,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - [#247](https://github.com/nf-core/epitopeprediction/pull/247) - Update to nf-core template `3.0.2`
-- [#255](https://github.com/nf-core/epitopeprediction/pull/256) - Update to nf-core template `3.1.1`
+- [#255](https://github.com/nf-core/epitopeprediction/pull/256) - Update to nf-core template `3.1.2`
 
 ## v2.3.1 - Oesterberg - 2024-05-17
 
diff --git a/nextflow.config b/nextflow.config
index c256ff8..2fe4fb4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -228,14 +228,13 @@ env {
 }
 
 // Set bash options
-process.shell = """\
-bash
-
-set -e # Exit if a tool returns a non-zero status/exit code
-set -u # Treat unset variables and parameters as an error
-set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
-set -C # No clobber - prevent output redirection from overwriting files.
-"""
+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
+]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false