nf-core · muffato · Sep 30, 2025 · Sep 12, 2025 · Sep 12, 2025 · Sep 13, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -20,6 +20,8 @@
 
 ### Subworkflows
 
+- Linting of patched subworkflows ([#3755](https://github.com/nf-core/tools/pull/3755))
+
 ### General
 
 - don't read param expressions with spaces as params ([#3674](https://github.com/nf-core/tools/pull/3674))

diff --git a/nf_core/components/info.py b/nf_core/components/info.py
@@ -165,7 +165,7 @@ def get_component_info(self):
             self.meta = self.get_remote_yaml()
 
         # Could not find the meta
-        if self.meta is False:
+        if self.meta is None:
             raise UserWarning(f"Could not find {self.component_type[:-1]} '{self.component}'")
 
         return self.generate_component_info_help()

diff --git a/nf_core/subworkflows/lint/subworkflow_changes.py b/nf_core/subworkflows/lint/subworkflow_changes.py
@@ -42,7 +42,13 @@ def subworkflow_changes(subworkflow_lint_object, subworkflow):
                 with open(tempdir / file, "w") as fh:
                     fh.writelines(lines)
         except LookupError:
-            # This error is already reported by subworkflow_patch, so just return
+            subworkflow.failed.append(
+                (
+                    "subworkflow_patch",
+                    "Subworkflow patch cannot be cleanly applied",
+                    f"{subworkflow.component_dir}",
+                )
+            )
             return
     else:
         tempdir = subworkflow.component_dir

diff --git a/tests/subworkflows/test_lint.py b/tests/subworkflows/test_lint.py
@@ -1,5 +1,6 @@
 import json
 import shutil
+import subprocess
 from pathlib import Path
 
 import nf_core.subworkflows
@@ -434,3 +435,56 @@ def test_subworkflows_lint_local_old_format(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
+
+
+class TestSubworkflowsLintPatch(TestSubworkflows):
+    def setUp(self) -> None:
+        super().setUp()
+
+        # Install the subworkflow bam_sort_stats_samtools
+        self.subworkflow_install.install("bam_sort_stats_samtools")
+
+        # Modify the subworkflow by inserting a new input channel
+        new_line = "    ch_dummy // channel: [ path ]\n"
+
+        subworkflow_path = Path(self.pipeline_dir, "subworkflows", "nf-core", "bam_sort_stats_samtools", "main.nf")
+
+        with open(subworkflow_path) as fh:
+            lines = fh.readlines()
+        for line_index in range(len(lines)):
+            if "take:" in lines[line_index]:
+                lines.insert(line_index + 1, new_line)
+        with open(subworkflow_path, "w") as fh:
+            fh.writelines(lines)
+
+        # Create a patch file
+        self.patch_obj = nf_core.subworkflows.SubworkflowPatch(self.pipeline_dir)
+        self.patch_obj.patch("bam_sort_stats_samtools")
+
+    def test_lint_clean_patch(self):
+        """Test linting a patched subworkflow"""
+
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir)
+        subworkflow_lint.lint(print_results=False, subworkflow="bam_sort_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) == 0, f"Linting warned with {[x.__dict__ for x in subworkflow_lint.warned]}"
+
+    def test_lint_broken_patch(self):
+        """Test linting a patched subworkflow when the patch is broken"""
+
+        # Now modify the diff
+        diff_file = Path(
+            self.pipeline_dir, "subworkflows", "nf-core", "bam_sort_stats_samtools", "bam_sort_stats_samtools.diff"
+        )
+        subprocess.check_call(["sed", "-i''", "s/...$//", str(diff_file)])
+
+        subworkflow_lint = nf_core.subworkflows.SubworkflowLint(directory=self.pipeline_dir)
+        subworkflow_lint.lint(print_results=False, subworkflow="bam_sort_stats_samtools")
+
+        assert len(subworkflow_lint.failed) == 1, f"Linting failed with {[x.__dict__ for x in subworkflow_lint.failed]}"
+        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]}"
diff --git a/tests/subworkflows/test_patch.py b/tests/subworkflows/test_patch.py
@@ -55,7 +55,7 @@ def setup_patch(self, pipeline_dir, modify_subworkflow):
             self.modify_main_nf(subworkflow_path / "main.nf")
 
     def test_create_patch_no_change(self):
-        """Test creating a patch when there is a change to the module"""
+        """Test creating a patch when there is no change to the subworkflow"""
         self.setup_patch(self.pipeline_dir, False)
 
         # Try creating a patch file
@@ -69,7 +69,7 @@ def test_create_patch_no_change(self):
         assert not (subworkflow_path / "bam_sort_stats_samtools.diff").exists()
 
     def test_create_patch_change(self):
-        """Test creating a patch when there is no change to the subworkflow"""
+        """Test creating a patch when there is a change to the subworkflow"""
         self.setup_patch(self.pipeline_dir, True)
 
         # Try creating a patch file