From 0d8bfaeb893126ea484ad7ccd9d782e04df0dde8 Mon Sep 17 00:00:00 2001
From: yuxinNing <92061677+ningyuxin1999@users.noreply.github.com>
Date: Tue, 2 Sep 2025 11:54:22 +0000
Subject: [PATCH 01/12] start with process label checks

---
 nf_core/components/nfcore_component.py |  8 ++---
 nf_core/modules/lint/main_nf.py        |  9 +++--
 tests/modules/lint/test_main_nf.py     | 48 ++++++++++++++++++++------
 3 files changed, 45 insertions(+), 20 deletions(-)

diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 0acd2fafad..5d9d195eca 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -7,6 +7,8 @@
 from pathlib import Path
 from typing import Any, Optional, Union
 
+from reftrace import Module
+
 log = logging.getLogger(__name__)
 
 
@@ -179,11 +181,7 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st
         return included_components
 
     def _get_process_name(self):
-        with open(self.main_nf) as fh:
-            for line in fh:
-                if re.search(r"^\s*process\s*\w*\s*{", line):
-                    return re.search(r"^\s*process\s*(\w*)\s*{.*", line).group(1) or ""
-        return ""
+        return Module.from_file(str(self.main_nf)).processes[0].name
 
     def get_inputs_from_main_nf(self) -> None:
         """Collect all inputs from the main.nf file."""
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 063fc354fa..162bd768e9 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -448,7 +448,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
         return docker_tag == singularity_tag
 
 
-def check_process_labels(self, lines):
+def check_process_labels(self, mod):
     correct_process_labels = [
         "process_single",
         "process_low",
@@ -457,14 +457,13 @@ def check_process_labels(self, lines):
         "process_long",
         "process_high_memory",
     ]
-    all_labels = [line.strip() for line in lines if line.lstrip().startswith("label ")]
+    label = mod.processes[0].labels[0]
+    all_labels = label.split()
     bad_labels = []
     good_labels = []
     if len(all_labels) > 0:
         for label in all_labels:
-            try:
-                label = re.match(r"^label\s+'?\"?([a-zA-Z0-9_-]+)'?\"?$", label).group(1)
-            except AttributeError:
+            if not label.replace("_", "").isalnum():
                 self.warned.append(
                     (
                         "process_standard_label",
diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py
index d4327f50f5..04f7649c7c 100644
--- a/tests/modules/lint/test_main_nf.py
+++ b/tests/modules/lint/test_main_nf.py
@@ -1,4 +1,7 @@
+from pathlib import Path
+
 import pytest
+from reftrace import Module, ParseError
 
 import nf_core.modules.lint
 import nf_core.modules.patch
@@ -7,33 +10,58 @@
 from ...test_modules import TestModules
 from .test_lint_utils import MockModuleLint
 
+# @pytest.mark.parametrize(
+#     "content,passed,warned,failed",
+#     [
+#         # Valid process label
+#         ("label 'process_high'\ncpus 12", 1, 0, 0),
+#         # Non-alphanumeric characters in label
+#         ("label 'a:label:with:colons'\ncpus 12", 0, 2, 0),
+#         # Conflicting labels
+#         ("label 'process_high'\nlabel 'process_low'\ncpus 12", 0, 1, 0),
+#         # Duplicate labels
+#         ("label 'process_high'\nlabel 'process_high'\ncpus 12", 0, 2, 0),
+#         # Valid and non-standard labels
+#         ("label 'process_high'\nlabel 'process_extra_label'\ncpus 12", 1, 1, 0),
+#         # Non-standard label only
+#         ("label 'process_extra_label'\ncpus 12", 0, 2, 0),
+#         # Non-standard duplicates without quotes
+#         ("label process_extra_label\nlabel process_extra_label\ncpus 12", 0, 3, 0),
+#         # No label found
+#         ("cpus 12", 0, 1, 0),
+#     ],
+# )
+
 
 @pytest.mark.parametrize(
     "content,passed,warned,failed",
     [
         # Valid process label
-        ("label 'process_high'\ncpus 12", 1, 0, 0),
+        ("process_high", 1, 0, 0),
         # Non-alphanumeric characters in label
-        ("label 'a:label:with:colons'\ncpus 12", 0, 2, 0),
+        ("a:label:with:colons", 0, 2, 0),
         # Conflicting labels
-        ("label 'process_high'\nlabel 'process_low'\ncpus 12", 0, 1, 0),
+        ("process_high process_low", 0, 1, 0),
         # Duplicate labels
-        ("label 'process_high'\nlabel 'process_high'\ncpus 12", 0, 2, 0),
+        ("process_high process_high", 0, 2, 0),
         # Valid and non-standard labels
-        ("label 'process_high'\nlabel 'process_extra_label'\ncpus 12", 1, 1, 0),
+        ("process_high process_extra_label", 1, 1, 0),
         # Non-standard label only
-        ("label 'process_extra_label'\ncpus 12", 0, 2, 0),
+        ("process_extra_label", 0, 2, 0),
         # Non-standard duplicates without quotes
-        ("label process_extra_label\nlabel process_extra_label\ncpus 12", 0, 3, 0),
+        ("process_extra_label process_extra_label", 0, 3, 0),
         # No label found
-        ("cpus 12", 0, 1, 0),
+        (" ", 0, 1, 0),
     ],
 )
 def test_process_labels(content, passed, warned, failed):
     """Test process label validation"""
     mock_lint = MockModuleLint()
-    check_process_labels(mock_lint, content.splitlines())
-
+    module = Module.from_file(str(Path(mock_lint.main_nf)))
+    assert not isinstance(module, ParseError)
+    assert len(module.processes) == 1
+    module.processes[0].labels[0] = content
+    check_process_labels(mock_lint, module)
     assert len(mock_lint.passed) == passed
     assert len(mock_lint.warned) == warned
     assert len(mock_lint.failed) == failed

From bbdfb1bfc7711c95909d879e683ba86e1f808872 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 2 Sep 2025 11:59:28 +0000
Subject: [PATCH 02/12] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7eaac6d521..04e81cfeba 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,7 @@
 
 - Support modules with `exec:` blocks ([#3633](https://github.com/nf-core/tools/pull/3633))
 - feat: nf-core modules bump-version supports specifying the toolkit ([#3608](https://github.com/nf-core/tools/pull/3608))
+- Testing out Reftrace for regex replacement in modules ([#3745](https://github.com/nf-core/tools/pull/3745))
 
 ### Subworkflows
 

From 5cb0d4fc1bbff356458efaa69a7f3b50aa8fe412 Mon Sep 17 00:00:00 2001
From: Edmund Miller <edmund.miller@seqera.io>
Date: Wed, 3 Sep 2025 17:07:28 -0500
Subject: [PATCH 03/12] feat: replace regex with Reftrace for process label
 parsing in module linting
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Replace regex-based process label validation with structured parsing using
the Reftrace library. This provides more accurate parsing of Nextflow syntax
and better error handling.

Key changes:
- Enhanced MockModuleLint to create temporary files for Reftrace compatibility
- Updated check_process_labels to use Reftrace Module objects instead of raw lines
- Modified integration to parse modules with Reftrace and handle parse errors
- Updated unit tests to create proper Nextflow syntax files for testing

Addresses Yuxin's challenge with integrating Reftrace into the testing
infrastructure while maintaining the existing linting functionality.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>
---
 nf_core/modules/lint/main_nf.py       | 45 ++++++++++++--
 tests/modules/lint/test_lint_utils.py | 30 ++++++++-
 tests/modules/lint/test_main_nf.py    | 88 ++++++++++++++++++++-------
 3 files changed, 135 insertions(+), 28 deletions(-)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index 162bd768e9..ed6954a0b5 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -268,8 +268,16 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
     else:
         self.failed.append(("process_capitals", "Process name is not in capital letters", self.main_nf))
 
-    # Check that process labels are correct
-    check_process_labels(self, lines)
+    # Check that process labels are correct using Reftrace
+    from reftrace import Module, ParseError
+
+    reftrace_mod = Module.from_file(str(self.main_nf))
+    if not isinstance(reftrace_mod, ParseError):
+        check_process_labels(self, reftrace_mod)
+    else:
+        self.failed.append(
+            ("process_standard_label", f"Failed to parse module with Reftrace: {reftrace_mod.error}", self.main_nf)
+        )
 
     # Deprecated enable_conda
     for i, raw_line in enumerate(lines):
@@ -449,6 +457,16 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
 
 
 def check_process_labels(self, mod):
+    """
+    Check process labels using Reftrace parsing.
+
+    This function validates that process labels conform to nf-core standards using
+    structured parsing via the Reftrace library.
+
+    Args:
+        self: ModuleLint object with passed/warned/failed lists and main_nf path
+        mod: Reftrace Module object containing parsed Nextflow processes
+    """
     correct_process_labels = [
         "process_single",
         "process_low",
@@ -457,10 +475,27 @@ def check_process_labels(self, mod):
         "process_long",
         "process_high_memory",
     ]
-    label = mod.processes[0].labels[0]
-    all_labels = label.split()
+
+    # Defensive checks for Reftrace module structure
+    if not mod.processes:
+        self.warned.append(("process_standard_label", "No processes found in module", self.main_nf))
+        return
+
+    process = mod.processes[0]
+    if not process.labels:
+        self.warned.append(("process_standard_label", "Process label not specified", self.main_nf))
+        return
+
+    # Extract label values from all label directives
+    all_labels = []
+    for label_directive in process.labels:
+        # Get the label value from Reftrace Label objects
+        if hasattr(label_directive, "value") and label_directive.value:
+            label_value = label_directive.value
+            all_labels.append(label_value)
     bad_labels = []
     good_labels = []
+    invalid_labels_count = 0
     if len(all_labels) > 0:
         for label in all_labels:
             if not label.replace("_", "").isalnum():
@@ -471,11 +506,13 @@ def check_process_labels(self, mod):
                         self.main_nf,
                     )
                 )
+                invalid_labels_count += 1
                 continue
             if label not in correct_process_labels:
                 bad_labels.append(label)
             else:
                 good_labels.append(label)
+
         if len(good_labels) > 1:
             self.warned.append(
                 (
diff --git a/tests/modules/lint/test_lint_utils.py b/tests/modules/lint/test_lint_utils.py
index 006bec978a..8cbb078b26 100644
--- a/tests/modules/lint/test_lint_utils.py
+++ b/tests/modules/lint/test_lint_utils.py
@@ -1,3 +1,6 @@
+import os
+import tempfile
+
 import nf_core.modules.lint
 
 from ...test_modules import TestModules
@@ -12,7 +15,32 @@ def __init__(self):
         self.warned = []
         self.failed = []
 
-        self.main_nf = "main_nf"
+        # Create a temporary file with basic Nextflow process structure
+        # that Reftrace can parse
+        self._temp_file = tempfile.NamedTemporaryFile(mode="w", suffix=".nf", delete=False)
+        basic_process = """process TEST_PROCESS {
+    label 'process_high'
+
+    input:
+    path input_file
+
+    output:
+    path "output.txt"
+
+    script:
+    '''
+    echo "test" > output.txt
+    '''
+}
+"""
+        self._temp_file.write(basic_process)
+        self._temp_file.close()
+        self.main_nf = self._temp_file.name
+
+    def cleanup(self):
+        """Clean up the temporary file"""
+        if hasattr(self, "_temp_file") and os.path.exists(self._temp_file.name):
+            os.unlink(self._temp_file.name)
 
 
 class TestModulesLint(TestModules):
diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py
index 04f7649c7c..748dcf8ed4 100644
--- a/tests/modules/lint/test_main_nf.py
+++ b/tests/modules/lint/test_main_nf.py
@@ -1,5 +1,3 @@
-from pathlib import Path
-
 import pytest
 from reftrace import Module, ParseError
 
@@ -34,37 +32,81 @@
 
 
 @pytest.mark.parametrize(
-    "content,passed,warned,failed",
+    "label_content,passed,warned,failed",
     [
         # Valid process label
-        ("process_high", 1, 0, 0),
+        ("label 'process_high'", 1, 0, 0),
         # Non-alphanumeric characters in label
-        ("a:label:with:colons", 0, 2, 0),
-        # Conflicting labels
-        ("process_high process_low", 0, 1, 0),
+        ("label 'a:label:with:colons'", 0, 2, 0),
+        # Conflicting labels (multiple label lines)
+        ("label 'process_high'\\n    label 'process_low'", 0, 1, 0),
         # Duplicate labels
-        ("process_high process_high", 0, 2, 0),
+        ("label 'process_high'\\n    label 'process_high'", 0, 2, 0),
         # Valid and non-standard labels
-        ("process_high process_extra_label", 1, 1, 0),
+        ("label 'process_high'\\n    label 'process_extra_label'", 1, 1, 0),
         # Non-standard label only
-        ("process_extra_label", 0, 2, 0),
-        # Non-standard duplicates without quotes
-        ("process_extra_label process_extra_label", 0, 3, 0),
+        ("label 'process_extra_label'", 0, 2, 0),
+        # Duplicate non-standard labels
+        ("label 'process_extra_label'\\n    label 'process_extra_label'", 0, 3, 0),
         # No label found
-        (" ", 0, 1, 0),
+        ("cpus 2", 0, 1, 0),
     ],
 )
-def test_process_labels(content, passed, warned, failed):
+def test_process_labels(label_content, passed, warned, failed):
     """Test process label validation"""
-    mock_lint = MockModuleLint()
-    module = Module.from_file(str(Path(mock_lint.main_nf)))
-    assert not isinstance(module, ParseError)
-    assert len(module.processes) == 1
-    module.processes[0].labels[0] = content
-    check_process_labels(mock_lint, module)
-    assert len(mock_lint.passed) == passed
-    assert len(mock_lint.warned) == warned
-    assert len(mock_lint.failed) == failed
+    # Create a temporary file with the specific label content
+    import os
+    import tempfile
+
+    # Create proper Nextflow content with the label
+    process_content = f"""process TEST_PROCESS {{
+    {label_content}
+
+    input:
+    path input_file
+
+    output:
+    path "output.txt"
+
+    script:
+    '''
+    echo "test" > output.txt
+    '''
+}}
+"""
+
+    temp_file = tempfile.NamedTemporaryFile(mode="w", suffix=".nf", delete=False)
+    temp_file.write(process_content)
+    temp_file.close()
+
+    try:
+        # Create MockModuleLint but override with our specific test file
+        mock_lint = MockModuleLint()
+        mock_lint.cleanup()  # Clean up the default temp file
+        mock_lint.main_nf = temp_file.name
+
+        # Parse with Reftrace
+        module = Module.from_file(temp_file.name)
+        assert not isinstance(module, ParseError), f"Failed to parse test file: {module}"
+
+        # Run the check_process_labels function
+        check_process_labels(mock_lint, module)
+
+        # Verify results
+        assert len(mock_lint.passed) == passed, (
+            f"Expected {passed} passed tests, got {len(mock_lint.passed)}: {mock_lint.passed}"
+        )
+        assert len(mock_lint.warned) == warned, (
+            f"Expected {warned} warned tests, got {len(mock_lint.warned)}: {mock_lint.warned}"
+        )
+        assert len(mock_lint.failed) == failed, (
+            f"Expected {failed} failed tests, got {len(mock_lint.failed)}: {mock_lint.failed}"
+        )
+
+    finally:
+        # Clean up the temporary file
+        if os.path.exists(temp_file.name):
+            os.unlink(temp_file.name)
 
 
 @pytest.mark.parametrize(

From 21c9eb753881e6eed85bff6f2ca693694b45cfa5 Mon Sep 17 00:00:00 2001
From: yuxinNing <92061677+ningyuxin1999@users.noreply.github.com>
Date: Mon, 8 Sep 2025 15:44:39 +0000
Subject: [PATCH 04/12] fix test

---
 nf_core/modules/lint/main_nf.py    | 2 +-
 tests/modules/lint/test_main_nf.py | 9 ++++-----
 2 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index ed6954a0b5..a887b19ea4 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -483,7 +483,7 @@ def check_process_labels(self, mod):
 
     process = mod.processes[0]
     if not process.labels:
-        self.warned.append(("process_standard_label", "Process label not specified", self.main_nf))
+        self.warned.append(("process_standard_label", "No label found for process", self.main_nf))
         return
 
     # Extract label values from all label directives
diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py
index 748dcf8ed4..b84b50b431 100644
--- a/tests/modules/lint/test_main_nf.py
+++ b/tests/modules/lint/test_main_nf.py
@@ -39,15 +39,15 @@
         # Non-alphanumeric characters in label
         ("label 'a:label:with:colons'", 0, 2, 0),
         # Conflicting labels (multiple label lines)
-        ("label 'process_high'\\n    label 'process_low'", 0, 1, 0),
+        ("label 'process_low'\nlabel 'process_high'", 0, 1, 0),
         # Duplicate labels
-        ("label 'process_high'\\n    label 'process_high'", 0, 2, 0),
+        ("label 'process_high'\nlabel 'process_high'", 0, 2, 0),
         # Valid and non-standard labels
-        ("label 'process_high'\\n    label 'process_extra_label'", 1, 1, 0),
+        ("label 'process_high'\nlabel 'process_extra_label'", 1, 1, 0),
         # Non-standard label only
         ("label 'process_extra_label'", 0, 2, 0),
         # Duplicate non-standard labels
-        ("label 'process_extra_label'\\n    label 'process_extra_label'", 0, 3, 0),
+        ("label 'process_extra_label'\nlabel 'process_extra_label'", 0, 3, 0),
         # No label found
         ("cpus 2", 0, 1, 0),
     ],
@@ -88,7 +88,6 @@ def test_process_labels(label_content, passed, warned, failed):
         # Parse with Reftrace
         module = Module.from_file(temp_file.name)
         assert not isinstance(module, ParseError), f"Failed to parse test file: {module}"
-
         # Run the check_process_labels function
         check_process_labels(mock_lint, module)
 

From a9a0b5e9ba2c7ec8ef2b1bf3dffc4de2be69df9f Mon Sep 17 00:00:00 2001
From: yuxinNing <92061677+ningyuxin1999@users.noreply.github.com>
Date: Tue, 23 Sep 2025 09:41:13 +0000
Subject: [PATCH 05/12] update requirement

---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index 15ae184b2d..d8245a79f8 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -24,3 +24,4 @@ textual==5.1.1
 trogon
 pdiff
 ruamel.yaml
+reftrace

From d88d9136268a42a824b465cab17b0f3c817d57b0 Mon Sep 17 00:00:00 2001
From: yuxinNing <92061677+ningyuxin1999@users.noreply.github.com>
Date: Tue, 23 Sep 2025 10:24:43 +0000
Subject: [PATCH 06/12] tempfile

---
 tests/modules/lint/test_lint_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/modules/lint/test_lint_utils.py b/tests/modules/lint/test_lint_utils.py
index 8cbb078b26..4f3a4ad3f6 100644
--- a/tests/modules/lint/test_lint_utils.py
+++ b/tests/modules/lint/test_lint_utils.py
@@ -60,4 +60,4 @@ def test_mock_module_lint(self):
         assert isinstance(mock_lint.passed, list)
         assert isinstance(mock_lint.warned, list)
         assert isinstance(mock_lint.failed, list)
-        assert mock_lint.main_nf == "main_nf"
+        assert mock_lint.main_nf == mock_lint._temp_file.name

From 4de14dc6dab053b5f0b0add106bd54dea0d50c6f Mon Sep 17 00:00:00 2001
From: yuxinNing <92061677+ningyuxin1999@users.noreply.github.com>
Date: Tue, 23 Sep 2025 12:24:22 +0000
Subject: [PATCH 07/12] debug

---
 nf_core/components/nfcore_component.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 5d9d195eca..b4c54ccd8a 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -181,8 +181,11 @@ def _get_included_components_in_chained_tests(self, main_nf_test: Union[Path, st
         return included_components
 
     def _get_process_name(self):
-        return Module.from_file(str(self.main_nf)).processes[0].name
-
+        try:
+            return Module.from_file(str(self.main_nf)).processes[0].name
+        except IndexError:
+            return ""
+        
     def get_inputs_from_main_nf(self) -> None:
         """Collect all inputs from the main.nf file."""
         inputs: Any = []  # Can be 'list[list[dict[str, dict[str, str]]]]' or 'list[str]'

From 1c57ed9ae2c68698d94137fa458dd433d571978d Mon Sep 17 00:00:00 2001
From: yuxinNing <ningyuxin1999@126.com>
Date: Mon, 27 Oct 2025 13:45:50 +0100
Subject: [PATCH 08/12] removing requirement

---
 requirements.txt | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/requirements.txt b/requirements.txt
index fb16a9d518..c19a8183e9 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -22,6 +22,5 @@ repo2rocrate
 tabulate
 textual==6.2.1
 trogon
-pdiff
+ipdiff
 ruamel.yaml
-reftrace

From 4829bef37ab93566d266930a0645c0568e1aac16 Mon Sep 17 00:00:00 2001
From: yuxinNing <92061677+ningyuxin1999@users.noreply.github.com>
Date: Mon, 27 Oct 2025 14:10:28 +0000
Subject: [PATCH 09/12] Pathlib

---
 .vscode/settings.json              | 5 ++++-
 nf_core/modules/lint/main_nf.py    | 6 ++----
 tests/modules/lint/test_main_nf.py | 7 ++++---
 3 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/.vscode/settings.json b/.vscode/settings.json
index 5651d52e08..30972c9c3b 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -12,5 +12,8 @@
             "source.fixAll": "explicit",
             "source.organizeImports": "explicit"
         }
-    }
+    },
+    "python-envs.defaultEnvManager": "ms-python.python:conda",
+    "python-envs.defaultPackageManager": "ms-python.python:conda",
+    "python-envs.pythonProjects": []
 }
diff --git a/nf_core/modules/lint/main_nf.py b/nf_core/modules/lint/main_nf.py
index a4631d9dd7..8e5b923f7b 100644
--- a/nf_core/modules/lint/main_nf.py
+++ b/nf_core/modules/lint/main_nf.py
@@ -10,6 +10,7 @@
 
 import requests
 import yaml
+from reftrace import Module, ParseError
 from rich.progress import Progress
 
 import nf_core
@@ -308,9 +309,6 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
     else:
         self.failed.append(("main_nf", "process_capitals", "Process name is not in capital letters", self.main_nf))
 
-    # Check that process labels are correct using Reftrace
-    from reftrace import Module, ParseError
-
     reftrace_mod = Module.from_file(str(self.main_nf))
     if not isinstance(reftrace_mod, ParseError):
         check_process_labels(self, reftrace_mod)
@@ -532,7 +530,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
         return docker_tag == singularity_tag
 
 
-def check_process_labels(self, mod):
+def check_process_labels(self, mod:Module):
     """
     Check process labels using Reftrace parsing.
 
diff --git a/tests/modules/lint/test_main_nf.py b/tests/modules/lint/test_main_nf.py
index b5a2abdd62..da0569b95b 100644
--- a/tests/modules/lint/test_main_nf.py
+++ b/tests/modules/lint/test_main_nf.py
@@ -1,3 +1,5 @@
+from pathlib import Path
+
 import pytest
 from reftrace import Module, ParseError
 
@@ -55,7 +57,6 @@
 def test_process_labels(label_content, passed, warned, failed):
     """Test process label validation"""
     # Create a temporary file with the specific label content
-    import os
     import tempfile
 
     # Create proper Nextflow content with the label
@@ -104,8 +105,8 @@ def test_process_labels(label_content, passed, warned, failed):
 
     finally:
         # Clean up the temporary file
-        if os.path.exists(temp_file.name):
-            os.unlink(temp_file.name)
+        if Path(temp_file.name).exists():
+            Path(temp_file.name).unlink()
 
 
 @pytest.mark.parametrize(

From f5c7e5702c8548d4a72feef7ac8919b3b94efb3e Mon Sep 17 00:00:00 2001
From: yuxinNing <92061677+ningyuxin1999@users.noreply.github.com>
Date: Mon, 27 Oct 2025 14:29:24 +0000
Subject: [PATCH 10/12] requirement

---
 requirements.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements.txt b/requirements.txt
index c19a8183e9..00de9ad08a 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -24,3 +24,4 @@ textual==6.2.1
 trogon
 ipdiff
 ruamel.yaml
+reftrace
\ No newline at end of file

From 64a99ba237a0bbf04f37c93e16172a3bdfbcdd15 Mon Sep 17 00:00:00 2001
From: yuxinNing <92061677+ningyuxin1999@users.noreply.github.com>
Date: Tue, 28 Oct 2025 09:50:19 +0000
Subject: [PATCH 11/12] test

---
 .vscode/settings.json                 | 5 +----
 tests/modules/lint/test_lint_utils.py | 2 +-
 2 files changed, 2 insertions(+), 5 deletions(-)

diff --git a/.vscode/settings.json b/.vscode/settings.json
index 30972c9c3b..5651d52e08 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -12,8 +12,5 @@
             "source.fixAll": "explicit",
             "source.organizeImports": "explicit"
         }
-    },
-    "python-envs.defaultEnvManager": "ms-python.python:conda",
-    "python-envs.defaultPackageManager": "ms-python.python:conda",
-    "python-envs.pythonProjects": []
+    }
 }
diff --git a/tests/modules/lint/test_lint_utils.py b/tests/modules/lint/test_lint_utils.py
index 4f3a4ad3f6..3cab90d33b 100644
--- a/tests/modules/lint/test_lint_utils.py
+++ b/tests/modules/lint/test_lint_utils.py
@@ -24,7 +24,7 @@ def __init__(self):
     input:
     path input_file
 
-    output:
+        output:
     path "output.txt"
 
     script:

From 2b358f489b1ba40b5d72c5433116c055ed297121 Mon Sep 17 00:00:00 2001
From: yuxinNing <92061677+ningyuxin1999@users.noreply.github.com>
Date: Tue, 28 Oct 2025 10:33:07 +0000
Subject: [PATCH 12/12] fix typo

---
 requirements.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/requirements.txt b/requirements.txt
index 00de9ad08a..4af22b2294 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -22,6 +22,6 @@ repo2rocrate
 tabulate
 textual==6.2.1
 trogon
-ipdiff
+pdiff
 ruamel.yaml
 reftrace
\ No newline at end of file