nf-core · mashehu · Apr 14, 2026 · Apr 1, 2026 · Apr 14, 2026 · Apr 14, 2026
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
@@ -244,7 +244,7 @@ def main_nf(
                 ("main_nf", "main_nf_version_topic", "Module emits software versions as topic", module.main_nf)
             )
         else:
-            module.warned.append(
+            module.failed.append(
                 ("main_nf", "main_nf_version_topic", "Module does not emit software versions as topic", module.main_nf)
             )
 

diff --git a/nf_core/subworkflows/lint/main_nf.py b/nf_core/subworkflows/lint/main_nf.py
@@ -106,22 +106,6 @@ def main_nf(_, subworkflow: NFCoreComponent) -> tuple[list[str], list[str]]:
     # Check the main definition
     check_main_section(subworkflow, main_lines, included_components)
 
-    # Check that a software version is emitted
-    if outputs:
-        if "versions" in outputs:
-            subworkflow.passed.append(
-                ("main_nf", "main_nf_version_emitted", "Subworkflow emits software version", subworkflow.main_nf)
-            )
-        else:
-            subworkflow.warned.append(
-                (
-                    "main_nf",
-                    "main_nf_version_emitted",
-                    "Subworkflow does not emit software version. Can be ignored if the subworkflow is using topic channels",
-                    subworkflow.main_nf,
-                )
-            )
-
     return inputs, outputs
 
 
@@ -167,24 +151,6 @@ def check_main_section(self, lines, included_components):
                         self.main_nf,
                     )
                 )
-            if component + ".out.versions" in script:
-                self.passed.append(
-                    (
-                        "main_nf",
-                        "main_nf_include_versions",
-                        f"Included component '{component}' versions are added in main.nf",
-                        self.main_nf,
-                    )
-                )
-            else:
-                self.warned.append(
-                    (
-                        "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",
-                        self.main_nf,
-                    )
-                )
 
 
 def check_subworkflow_section(self, lines: list[str]) -> list[str]:

diff --git a/nf_core/subworkflows/lint/subworkflow_tests.py b/nf_core/subworkflows/lint/subworkflow_tests.py
@@ -219,24 +219,6 @@ def subworkflow_tests(_, subworkflow: NFCoreComponent, allow_missing: bool = Fal
                                             snap_file,
                                         )
                                     )
-                            if "versions" in str(snap_content[test_name]) or "versions" in str(snap_content.keys()):
-                                subworkflow.passed.append(
-                                    (
-                                        "subworkflow_tests",
-                                        "test_snap_versions",
-                                        "versions found in snapshot file",
-                                        snap_file,
-                                    )
-                                )
-                            else:
-                                subworkflow.warned.append(
-                                    (
-                                        "subworkflow_tests",
-                                        "test_snap_versions",
-                                        "versions not found in snapshot file. Can be ignored if the subworkflow is using topic channels",
-                                        snap_file,
-                                    )
-                                )
                         except json.decoder.JSONDecodeError as e:
                             subworkflow.failed.append(
                                 (

diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py
@@ -149,9 +149,8 @@ def test_topics_and_emits_version_check(self):
             directory=self.pipeline_dir, remote_url=GITLAB_URL, branch=GITLAB_NFTEST_BRANCH
         )
         module_lint.lint(print_results=False, module="fastqc")
-        assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
-        assert any(w.lint_test in ("main_nf_version_emit", "main_nf_version_topic") for w in module_lint.warned), (
-            f"Expected warning about missing version topic, got {[w.message for w in module_lint.warned]}"
+        assert any(f.lint_test in ("main_nf_version_emit", "main_nf_version_topic") for f in module_lint.failed), (
+            f"Expected failure about missing version topic, got {[f.message for f in module_lint.failed]}"
         )
         assert len(module_lint.passed) > 0
 

diff --git a/tests/modules/lint/test_module_lint_remotes.py b/tests/modules/lint/test_module_lint_remotes.py
@@ -27,7 +27,7 @@ def test_modules_lint_gitlab_modules(self):
         self.mods_install_gitlab.install("multiqc")
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.pipeline_dir, remote_url=GITLAB_URL)
         module_lint.lint(print_results=False, all_modules=True)
-        assert len(module_lint.failed) == 2
+        assert len(module_lint.failed) == 3
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
 

diff --git a/tests/modules/lint/test_module_tests.py b/tests/modules/lint/test_module_tests.py
@@ -132,14 +132,15 @@ def test_nftest_failing_linting(self):
         Repo.clone_from(GITLAB_URL, self.nfcore_modules, branch=GITLAB_NFTEST_BRANCH)
 
         module_lint = nf_core.modules.lint.ModuleLint(directory=self.nfcore_modules)
-        module_lint.lint(print_results=False, module="kallisto/quant")
+        module_lint.lint(print_results=True, module="kallisto/quant")
 
-        assert len(module_lint.failed) == 2, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.failed) == 3, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) >= 0
         assert len(module_lint.warned) >= 0
-        assert module_lint.failed[0].lint_test == "meta_yml_valid"
-        assert module_lint.failed[1].lint_test == "test_main_tags"
-        assert "kallisto/index" in module_lint.failed[1].message
+        assert module_lint.failed[0].lint_test == "main_nf_version_topic"
+        assert module_lint.failed[1].lint_test == "meta_yml_valid"
+        assert module_lint.failed[2].lint_test == "test_main_tags"
+        assert "kallisto/index" in module_lint.failed[2].message
 
     def test_modules_absent_version(self):
         """Test linting a nf-test module if the versions is absent in the snapshot file `"""

diff --git a/tests/modules/lint/test_patch.py b/tests/modules/lint/test_patch.py
@@ -55,6 +55,6 @@ def test_modules_lint_patched_modules(self):
                 all_modules=True,
             )
 
-        assert len(module_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
+        assert len(module_lint.failed) == 2, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
         assert len(module_lint.passed) > 0
         assert len(module_lint.warned) >= 0
diff --git a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg