nf-core · mirpedrol · Aug 26, 2025 · Aug 26, 2025 · Aug 26, 2025 · Aug 27, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -27,6 +27,7 @@
 - Replace arm profile with arm64 and emulate_amd64 profiles ([#3689](https://github.com/nf-core/tools/pull/3689))
 - Remove workflow.trace from nf-test snapshot ([#3721](https://github.com/nf-core/tools/pull/3721))
 - Add GHA to update template nf-test snapshots ([#3723](https://github.com/nf-core/tools/pull/3723))
+- add pytest for get_wf_files ([#3725](https://github.com/nf-core/tools/pull/3725))
 
 ## [v3.3.2 - Tungsten Tamarin Patch 2](https://github.com/nf-core/tools/releases/tag/3.3.2) - [2025-07-08]
 

diff --git a/nf_core/utils.py b/nf_core/utils.py
@@ -1573,13 +1573,18 @@ def get_wf_files(wf_path: Path):
     """Return a list of all files in a directory (ignores .gitigore files)"""
 
     wf_files = []
-
     try:
         with open(Path(wf_path, ".gitignore")) as f:
             lines = f.read().splitlines()
-        ignore = [line for line in lines if line and not line.startswith("#")]
+            print(lines)
+        ignore = [
+            (str(wf_path / line) + "*" if line.endswith("/") else str(wf_path / line))
+            for line in lines
+            if line and not line.startswith("#")
+        ]
     except FileNotFoundError:
         ignore = []
+    print(ignore)
 
     for path in Path(wf_path).rglob("*"):
         if any(fnmatch.fnmatch(str(path), pattern) for pattern in ignore):

diff --git a/tests/test_utils.py b/tests/test_utils.py
@@ -212,10 +212,10 @@ def test_set_wd(self):
 
     def test_set_wd_revert_on_raise(self):
         wd_before_context = Path().resolve()
-        with pytest.raises(Exception):
-            with nf_core.utils.set_wd(self.tmp_dir):
-                raise Exception
-        assert wd_before_context == Path().resolve()
+        with mock.patch("nf_core.utils.set_wd", side_effect=Exception("mocked exception")):
+            with pytest.raises(Exception):
+                with nf_core.utils.set_wd(self.tmp_dir):
+                    assert wd_before_context == Path().resolve()
 
     @mock.patch("nf_core.utils.run_cmd")
     def test_fetch_wf_config(self, mock_run_cmd):
@@ -224,3 +224,16 @@ def test_fetch_wf_config(self, mock_run_cmd):
         config = nf_core.utils.fetch_wf_config(".", False)
         assert len(config.keys()) == 1
         assert "params.param2" in list(config.keys())
+
+    def test_get_wf_files(self):
+        (self.pipeline_obj.wf_path / "work").mkdir()
+        (self.pipeline_obj.wf_path / "work" / "file.txt").touch()
+        (self.pipeline_obj.wf_path / ".nextflow.log").touch()
+        files = nf_core.utils.get_wf_files(self.pipeline_obj.wf_path)
+        assert str(Path(self.pipeline_dir, "main.nf")) in files
+        assert str(Path(self.pipeline_dir, "work", "file.txt")) not in files
+        assert str(Path(self.pipeline_dir, ".nextflow.log")) not in files
+
+    def test_get_wf_files_no_gitignore(self):
+        files = nf_core.utils.get_wf_files(Path("random/path"))
+        assert files == []