mashehu · Nov 6, 2026 · Nov 6, 2026 · Nov 6, 2026
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,7 @@
 ### Linting
 
 - make pipelines linting, including ro-create also work offline ([#4585](https://github.com/nf-core/tools/pull/4585))
+- respect `skip_features` for `files_unchanged` tests ([#4596](https://github.com/nf-core/tools/pull/4596))
 
 ### Modules
 

diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py
@@ -26,7 +26,7 @@
 from nf_core import __version__
 from nf_core.components.lint import ComponentLint
 from nf_core.pipelines.lint_utils import console
-from nf_core.utils import NFCoreYamlLintConfig, strip_ansi_codes
+from nf_core.utils import NFCoreTemplateConfig, NFCoreYamlLintConfig, strip_ansi_codes
 from nf_core.utils import plural_s as _s
 
 from .actions_awsfulltest import actions_awsfulltest
@@ -123,6 +123,7 @@ def __init__(
         super().__init__(wf_path)
 
         self.lint_config: NFCoreYamlLintConfig | None = None
+        self.template_config: NFCoreTemplateConfig | None = None
         self.release_mode = release_mode
         self.fail_ignored = fail_ignored
         self.fail_warned = fail_warned
@@ -189,6 +190,7 @@ def _load_lint_config(self) -> bool:
         """
         _, tools_config = nf_core.utils.load_tools_config(self.wf_path)
         self.lint_config = getattr(tools_config, "lint", None) or None
+        self.template_config = getattr(tools_config, "template", None)
         is_correct = True
         # Check if we have any keys that don't match lint test names
         if self.lint_config is not None:

diff --git a/nf_core/pipelines/lint/files_unchanged.py b/nf_core/pipelines/lint/files_unchanged.py
@@ -119,11 +119,14 @@ def files_unchanged(self) -> dict[str, list[str] | bool]:
         names = ", ".join(c.get("name", "") for c in contributors if c.get("name"))
     else:
         names = manifest_config.get("author", "")
+    # Render the comparison with the pipeline's skipped features, so feature-dependent template content matches
+    skip_features = self.template_config.skip_features if self.template_config else None
     template_yaml = {
         "name": short_name,
         "description": manifest_config.get("description", ""),
         "author": names,
         "org": prefix,
+        "skip_features": skip_features or [],
     }
 
     template_yaml_path = Path(tmp_dir, "template.yaml")

diff --git a/tests/pipelines/lint/test_files_unchanged.py b/tests/pipelines/lint/test_files_unchanged.py
@@ -1,6 +1,8 @@
 from pathlib import Path
 from unittest import mock
 
+import yaml
+
 import nf_core.pipelines.lint

 from ..test_lint import TestLint
@@ -30,3 +32,19 @@ def test_files_unchanged_fail(self):
         assert len(results["failed"]) > 0
         assert str(failing_file) in results["failed"][0]
         assert results["could_fix"]
+
+    def test_files_unchanged_respects_skip_features(self):
+        """The comparison copy is rendered with the pipeline's skip_features"""
+        new_pipeline = self._make_pipeline_copy()
+        config_fn = Path(new_pipeline, ".nf-core.yml")
+        config = yaml.safe_load(config_fn.read_text())
+        config["template"]["skip_features"] = ["rocrate"]
+        config_fn.write_text(yaml.safe_dump(config))
+        # Without rocrate, the template's .prettierignore has no ro-crate entry
+        prettierignore = Path(new_pipeline, ".prettierignore")
+        prettierignore.write_text(prettierignore.read_text().replace("ro-crate-metadata.json\n", ""))
+
+        lint_obj = nf_core.pipelines.lint.PipelineLint(new_pipeline)
+        lint_obj._load()
+        results = lint_obj.files_unchanged()
+        assert len(results.get("failed", [])) == 0