diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 05a9599eb..9db8f3bfe 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -89,11 +89,6 @@ process {
 }
 {%- endif %}
 
-{% if modules -%}
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
-{%- endif %}
-
 profiles {
     debug {
         dumpHashes              = true
@@ -336,3 +331,8 @@ validation {
     }{% endif %}
 }
 {%- endif %}
+
+{% if modules -%}
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
+{%- endif %}