From b08466978169692c6f1db11511fe5f8efccac717 Mon Sep 17 00:00:00 2001
From: Ammar Aziz <spidermine63@gmail.com>
Date: Thu, 15 Jan 2026 23:33:33 +1100
Subject: [PATCH] added helpful comment for common gotcha - prefix scoping

---
 nf_core/module-template/main.nf | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/nf_core/module-template/main.nf b/nf_core/module-template/main.nf
index 49802b58c9..fd04aa8802 100644
--- a/nf_core/module-template/main.nf
+++ b/nf_core/module-template/main.nf
@@ -78,6 +78,9 @@ process {{ component_name_underscore|upper }} {
     script:
     def args = task.ext.args ?: ''
     {% if has_meta -%}
+    // TODO nf-core: The $prefix variable as defined below is ONLY available within the script block.
+    //               If $prefix is required elsewhere (eg in output block), remove the def keyword.
+    //               For further information on variable scope see https://midnighter.github.io/nextflow-gotchas/gotchas/variable-scope/
     def prefix = task.ext.prefix ?: "${meta.id}"
     {%- endif %}
     {% if not_empty_template -%}