diff --git a/CHANGELOG.md b/CHANGELOG.md
index 08c0ea6ae4..ad646d22a6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -20,6 +20,8 @@
 
 ### Linting
 
+- fix test for linting for version.yml ([#3947](https://github.com/nf-core/tools/pull/3947))
+
 ### Modules
 
 ### Subworkflows
diff --git a/nf_core/subworkflows/lint/main_nf.py b/nf_core/subworkflows/lint/main_nf.py
index 2167cd20da..cb2177ed5d 100644
--- a/nf_core/subworkflows/lint/main_nf.py
+++ b/nf_core/subworkflows/lint/main_nf.py
@@ -169,7 +169,7 @@ def check_main_section(self, lines, included_components):
                     (
                         "main_nf",
                         "main_nf_include_versions",
-                        f"Included component '{component}' versions are not added in main.nf Can be ignored if the module is using topic channels",
+                        f"Included component '{component}' versions are not added in main.nf. Can be ignored if the module is using topic channels",
                         self.main_nf,
                     )
                 )
diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py
index 31b54b9466..a68c42619f 100644
--- a/tests/modules/lint/test_main_nf.py
+++ b/tests/modules/lint/test_main_nf.py
@@ -137,9 +137,10 @@ def test_main_nf_lint_with_alternative_registry(self):
     def test_topics_and_emits_version_check(self):
         """Test that main_nf version emit and topics check works correctly"""
 
+        self.mods_install.install("bioawk")
         # Lint a module known to have versions YAML in main.nf (for now)
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir)
-        module_lint.lint(print_results=False, module="samtools/sort")
+        module_lint.lint(print_results=False, module="bioawk")
         assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.warned) == 2, (
             f"Linting warned with {[x.__dict__ for x in module_lint.warned]}, expected 2 warnings"
diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py
index 54ad7e7fc7..a092cd3c37 100644
--- a/tests/subworkflows/test_lint.py
+++ b/tests/subworkflows/test_lint.py
@@ -228,19 +228,19 @@ def test_subworkflows_lint_include_multiple_alias(self):
         subworkflow_lint.lint(print_results=False, subworkflow="bam_stats_samtools")
         assert len(subworkflow_lint.failed) >= 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
         assert len(subworkflow_lint.passed) > 0
-        assert len(subworkflow_lint.warned) == 2
-        assert any(
-            [
-                x.message == "Included component 'SAMTOOLS_STATS_1' versions are added in main.nf"
-                for x in subworkflow_lint.passed
-            ]
-        )
+        assert len(subworkflow_lint.warned) == 3
         assert any(
             [x.message == "Included component 'SAMTOOLS_STATS_1' used in main.nf" for x in subworkflow_lint.passed]
         )
         assert any(
             [x.message == "Included component 'SAMTOOLS_STATS_2' not used in main.nf" for x in subworkflow_lint.warned]
         )
+        assert any(
+            [
+                x.message.endswith("Can be ignored if the module is using topic channels")
+                for x in subworkflow_lint.warned
+            ]
+        )
 
         # cleanup
         self.subworkflow_remove.remove("bam_stats_samtools", force=True)
@@ -469,7 +469,13 @@ def test_lint_clean_patch(self):
 
         assert len(subworkflow_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
         assert len(subworkflow_lint.passed) > 0
-        assert len(subworkflow_lint.warned) == 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
+        assert len(subworkflow_lint.warned) == 1, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
+        assert any(
+            [
+                x.message.endswith("Can be ignored if the module is using topic channels")
+                for x in subworkflow_lint.warned
+            ]
+        )
 
     def test_lint_broken_patch(self):
         """Test linting a patched subworkflow when the patch is broken"""
@@ -487,4 +493,10 @@ def test_lint_broken_patch(self):
         errors = [x.message for x in subworkflow_lint.failed]
         assert "Subworkflow patch cannot be cleanly applied" in errors
         assert len(subworkflow_lint.passed) > 0
-        assert len(subworkflow_lint.warned) == 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
+        assert len(subworkflow_lint.warned) == 1, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
+        assert any(
+            [
+                x.message.endswith("Can be ignored if the module is using topic channels")
+                for x in subworkflow_lint.warned
+            ]
+        )