nf-core · mirpedrol · Oct 9, 2025 · Oct 7, 2025 · Oct 8, 2025 · Oct 8, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -23,6 +23,8 @@
 - do not check pytest_modules.yml file, deprecating ([#3748](https://github.com/nf-core/tools/pull/3748))
 - Use the org from the .nf-core.yml when linting manifest name and homePage. ([#3767](https://github.com/nf-core/tools/pull/3767))
 - Use the org from .nf-core.yml when linting multiqc_config report_comment ([#3800](https://github.com/nf-core/tools/pull/3800))
+- Linting of patched subworkflows ([#3755](https://github.com/nf-core/tools/pull/3755))
+- Add link to modules and subworkflows linting error docs ([#3818](https://github.com/nf-core/tools/pull/3818))
 
 ### Modules
 
@@ -32,7 +34,6 @@
 
 ### Subworkflows
 
-- Linting of patched subworkflows ([#3755](https://github.com/nf-core/tools/pull/3755))
 - Update the utils_nfschema_plugin subworkflow to the latest version ([#3814](https://github.com/nf-core/tools/pull/3814))
 
 ### General

diff --git a/nf_core/components/lint/__init__.py b/nf_core/components/lint/__init__.py
@@ -10,14 +10,14 @@
 from typing import Optional, Union
 
 import rich.box
-import rich.console
 import rich.panel
 import rich.repr
 from rich.markdown import Markdown
 from rich.table import Table
 
 import nf_core.modules.modules_utils
 import nf_core.utils
+from nf_core import __version__
 from nf_core.components.components_command import ComponentCommand
 from nf_core.components.nfcore_component import NFCoreComponent
 from nf_core.modules.modules_json import ModulesJson
@@ -38,9 +38,12 @@ class LintExceptionError(Exception):
 class LintResult:
     """An object to hold the results of a lint test"""
 
-    def __init__(self, component: NFCoreComponent, lint_test: str, message: str, file_path: Path):
+    def __init__(
+        self, component: NFCoreComponent, parent_lint_test: str, lint_test: str, message: str, file_path: Path
+    ):
         self.component = component
         self.lint_test = lint_test
+        self.parent_lint_test = parent_lint_test
         self.message = message
         self.file_path = file_path
         self.component_name: str = component.component_name
@@ -251,14 +254,14 @@ def _print_results(self, show_passed=False, sort_by="test"):
                 pass
 
         # Helper function to format test links nicely
-        def format_result(test_results, table):
+        def format_result(test_results: list[LintResult], table: Table) -> Table:
             """
-            Given an list of error message IDs and the message texts, return a nicely formatted
+            Given a LintResult object, return a nicely formatted
             string for the terminal with appropriate ASCII colours.
             """
             # TODO: Row styles don't work current as table-level style overrides.
             # Leaving it here in case there is a future fix
-            last_modname = False
+            last_modname = ""
             even_row = False
             for lint_result in test_results:
                 if last_modname and lint_result.component_name != last_modname:
@@ -276,10 +279,16 @@ def format_result(test_results, table):
                 file_path = os.path.relpath(lint_result.file_path, self.directory)
                 file_path_link = f"[link=vscode://file/{os.path.abspath(file_path)}]{file_path}[/link]"
 
+                # Add link to the test documentation
+                tools_version = __version__
+                if "dev" in __version__:
+                    tools_version = "dev"
+                test_link_message = f"[{lint_result.lint_test}](https://nf-co.re/docs/nf-core-tools/api_reference/{tools_version}/{self.component_type[:-1]}_lint_tests/{lint_result.parent_lint_test}): {lint_result.message}"
+
                 table.add_row(
                     module_name,
                     file_path_link,
-                    Markdown(f"{lint_result.message}"),
+                    Markdown(test_link_message),
                     style="dim" if even_row else None,
                 )
             return table
@@ -343,7 +352,7 @@ def format_result(test_results, table):
                 )
             )
 
-    def print_summary(self):
+    def print_summary(self) -> None:
         """Print a summary table to the console."""
         table = Table(box=rich.box.ROUNDED)
         table.add_column("[bold green]LINT RESULTS SUMMARY", no_wrap=True)

diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
@@ -47,9 +47,9 @@ def __init__(
         self.component_dir = component_dir
         self.repo_type = repo_type
         self.base_dir = base_dir
-        self.passed: list[tuple[str, str, Path]] = []
-        self.warned: list[tuple[str, str, Path]] = []
-        self.failed: list[tuple[str, str, Path]] = []
+        self.passed: list[tuple[str, str, str, Path]] = []
+        self.warned: list[tuple[str, str, str, Path]] = []
+        self.failed: list[tuple[str, str, str, Path]] = []
         self.inputs: list[list[dict[str, dict[str, str]]]] = []
         self.outputs: list[str] = []
         self.has_meta: bool = False

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
@@ -17,8 +17,6 @@
 import rich.progress
 import ruamel.yaml
 
-import nf_core.components
-import nf_core.components.nfcore_component
 import nf_core.modules.modules_utils
 import nf_core.utils
 from nf_core.components.components_utils import get_biotools_id, get_biotools_response, yaml

diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py
@@ -5,7 +5,7 @@
 import ruamel.yaml
 from jsonschema import exceptions, validators
 
-from nf_core.components.lint import ComponentLint, LintExceptionError, LintResult
+from nf_core.components.lint import ComponentLint, LintExceptionError
 from nf_core.components.nfcore_component import NFCoreComponent
 
 log = logging.getLogger(__name__)
@@ -38,6 +38,7 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent,
         if allow_missing:
             module.warned.append(
                 (
+                    "environment_yml",
                     "environment_yml_exists",
                     "Module's `environment.yml` does not exist",
                     Path(module.component_dir, "environment.yml"),
@@ -64,19 +65,32 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent,
         if env_yml is None:
             raise ruamel.yaml.scanner.ScannerError("Empty YAML file")
 
-        module.passed.append(("environment_yml_exists", "Module's `environment.yml` exists", module.environment_yml))
+        module.passed.append(
+            (
+                "environment_yml",
+                "environment_yml_exists",
+                "Module's `environment.yml` exists",
+                module.environment_yml,
+            )
+        )
 
     except FileNotFoundError:
         # check if the module's main.nf requires a conda environment
         with open(Path(module.component_dir, "main.nf")) as fh:
             main_nf = fh.read()
             if 'conda "${moduleDir}/environment.yml"' in main_nf:
                 module.failed.append(
-                    ("environment_yml_exists", "Module's `environment.yml` does not exist", module.environment_yml)
+                    (
+                        "environment_yml",
+                        "environment_yml_exists",
+                        "Module's `environment.yml` does not exist",
+                        module.environment_yml,
+                    )
                 )
             else:
                 module.passed.append(
                     (
+                        "environment_yml",
                         "environment_yml_exists",
                         "Module's `environment.yml` does not exist, but it is also not included in the main.nf",
                         module.environment_yml,
@@ -91,7 +105,12 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent,
                 schema = json.load(fh)
             validators.validate(instance=env_yml, schema=schema)
             module.passed.append(
-                ("environment_yml_valid", "Module's `environment.yml` is valid", module.environment_yml)
+                (
+                    "environment_yml",
+                    "environment_yml_valid",
+                    "Module's `environment.yml` is valid",
+                    module.environment_yml,
+                )
             )
             valid_env_yml = True
         except exceptions.ValidationError as e:
@@ -102,6 +121,7 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent,
                 e.message = e.schema["message"]
             module.failed.append(
                 (
+                    "environment_yml",
                     "environment_yml_valid",
                     f"The `environment.yml` of the module {module.component_name} is not valid: {e.message}.{hint}",
                     module.environment_yml,
@@ -155,9 +175,9 @@ def sort_key(x):
                 is_sorted = True
 
             if is_sorted:
-                module_lint_object.passed.append(
-                    LintResult(
-                        module,
+                module.passed.append(
+                    (
+                        "environment_yml",
                         "environment_yml_sorted",
                         "The dependencies in the module's `environment.yml` are sorted correctly",
                         module.environment_yml,
@@ -189,9 +209,9 @@ def sort_key(x):
                     # Then dump the sorted YAML
                     yaml.dump(env_yml, fh)
 
-                module_lint_object.passed.append(
-                    LintResult(
-                        module,
+                module.passed.append(
+                    (
+                        "environment_yml",
                         "environment_yml_sorted",
                         "The dependencies in the module's `environment.yml` have been sorted",
                         module.environment_yml,