diff --git a/.github/scripts/get_module_path.js b/.github/scripts/get_module_path.js
index a1d12929758..2fb939d072b 100644
--- a/.github/scripts/get_module_path.js
+++ b/.github/scripts/get_module_path.js
@@ -50,8 +50,10 @@ function run({ github, context }) {
         const result = get_module_names(files);
         console.log('Processed result:', result);
 
-        // Return stringified result for GitHub Actions output
-        return JSON.stringify(result);
+        // Ensure we're returning a properly formatted JSON string
+        const jsonResult = JSON.stringify(result);
+        console.log('Final JSON output:', jsonResult);
+        return jsonResult;
     } catch (error) {
         console.error("Error processing module paths:", error);
         console.error("Error details:", {
@@ -59,7 +61,6 @@ function run({ github, context }) {
             errorMessage: error.message,
             errorStack: error.stack
         });
-        // Return empty array instead of throwing
         return "[]";
     }
 }
diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml
index db2f77df1fd..a4eb0eddba5 100644
--- a/.github/workflows/lint.yml
+++ b/.github/workflows/lint.yml
@@ -90,7 +90,8 @@ jobs:
       - name: debug
         run: |
           echo "Modules files: ${{ steps.filter.outputs.modules_files }}"
-          echo "Module names: ${{ steps.module_names.outputs.result }}"
+          echo "Module names: ${{ fromJson(steps.module_names.outputs.result) }}"
+          echo "Raw module names output: ${{ steps.module_names.outputs.result }}"
 
   nf-core-lint-modules:
     runs-on: ${{ github.event.inputs.runners  || 'self-hosted' }}