diff --git a/.prettierignore b/.prettierignore
index f4a0781a1b..73e4c4e278 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -8,6 +8,7 @@ nf_core/pipeline-template/nextflow_schema.json
 nf_core/pipeline-template/modules.json
 nf_core/pipeline-template/tower.yml
 nf_core/pipeline-template/.github/ISSUE_TEMPLATE/bug_report.yml
+nf_core/pipeline-template/.github/workflows/nf-test.yml
 tests/data/pipeline_create_template_skip.yml
 # don't run on things handled by ruff
 *.py
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8f862b368a..1cacdee501 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,11 @@
 # nf-core/tools: Changelog
 
+## [v3.3.1 - Tungsten Tamarin Patch](https://github.com/nf-core/tools/releases/tag/3.3.1) - [2025-06-02]
+
+### Template
+
+- Use correct comment symbol in `nf-test.yml` ([#3601](https://github.com/nf-core/tools/pull/3601))
+
 ## [v3.3.0 - Tungsten Tamarin](https://github.com/nf-core/tools/releases/tag/3.3.0) - [2025-06-02]
 
 **Highlights**
diff --git a/nf_core/pipeline-template/.github/workflows/nf-test.yml b/nf_core/pipeline-template/.github/workflows/nf-test.yml
index 3960965c8c..a56df853f0 100644
--- a/nf_core/pipeline-template/.github/workflows/nf-test.yml
+++ b/nf_core/pipeline-template/.github/workflows/nf-test.yml
@@ -34,9 +34,9 @@ env:
 jobs:
   nf-test-changes:
     name: nf-test-changes
-    runs-on: // {% endraw %}{% if is_nfcore %}use self-hosted runners
+    runs-on: #{% endraw %}{% if is_nfcore %} use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test-changes
-      - runner=4cpu-linux-x64{% else %}use GitHub runners
+      - runner=4cpu-linux-x64{% else %} use GitHub runners
       - "ubuntu-latest"{% endif %}{% raw %}
     outputs:
       shard: ${{ steps.set-shards.outputs.shard }}
@@ -69,9 +69,9 @@ jobs:
     name: "${{ matrix.profile }} | ${{ matrix.NXF_VER }} | ${{ matrix.shard }}/${{ needs.nf-test-changes.outputs.total_shards }}"
     needs: [nf-test-changes]
     if: ${{ needs.nf-test-changes.outputs.total_shards != '0' }}
-    runs-on: // {% endraw %}{% if is_nfcore %}use self-hosted runners
+    runs-on: #{% endraw %}{% if is_nfcore %} use self-hosted runners
       - runs-on=${{ github.run_id }}-nf-test
-      - runner=4cpu-linux-x64{% else %}use GitHub runners
+      - runner=4cpu-linux-x64{% else %} use GitHub runners
       - "ubuntu-latest"{% endif %}{% raw %}
     strategy:
       fail-fast: false
@@ -111,9 +111,9 @@ jobs:
   confirm-pass:
     needs: [nf-test]
     if: always()
-    runs-on: // {% endraw %}{% if is_nfcore %}use self-hosted runners
+    runs-on:  {% endraw %}#{% if is_nfcore %} use self-hosted runners
       - runs-on=${{ github.run_id }}-confirm-pass
-      - runner=2cpu-linux-x64{% else %}use GitHub runners
+      - runner=2cpu-linux-x64{% else %} use GitHub runners
       - "ubuntu-latest"{% endif %}{% raw %}
     steps:
       - name: One or more tests failed
diff --git a/setup.py b/setup.py
index b9414cdfd3..cfbcf96d8c 100644
--- a/setup.py
+++ b/setup.py
@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-version = "3.3.0"
+version = "3.3.1"
 
 with open("README.md") as f:
     readme = f.read()