nf-core · mirpedrol · Nov 17, 2025 · Nov 14, 2025 · Nov 14, 2025 · Nov 17, 2025
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -37,6 +37,7 @@
 - TEMPLATE: ignore nf-core components during prettier linting ([#3858](https://github.com/nf-core/tools/pull/3858))
 - update json schema store URL ([#3877](https://github.com/nf-core/tools/pull/3877))
 - add word boundary for input, output and topic linting ([#3894](https://github.com/nf-core/tools/pull/3894))
+- Add linting of topics ([#3902](https://github.com/nf-core/tools/pull/3902))
 
 ### Modules
 

diff --git a/nf_core/components/create.py b/nf_core/components/create.py
@@ -534,7 +534,10 @@ def generate_meta_yml_file(self) -> None:
                     {"${task.process}": {"type": "string", "description": "The name of the process"}},
                     {f"{self.component}": {"type": "string", "description": "The name of the tool"}},
                     {
-                        f"{self.component} --version": {"type": "string", "description": "The version of the tool"},
+                        f"{self.component} --version": {
+                            "type": "eval",
+                            "description": "The expression to obtain the version of the tool",
+                        },
                     },
                 ]
             ]
@@ -543,12 +546,13 @@ def generate_meta_yml_file(self) -> None:
         versions_topic: dict[str, list | dict] = {
             "versions": [
                 [
-                    {"process": {"type": "string", "description": "The process the versions were collected from"}},
-                    {
-                        "tool": {"type": "string", "description": "The tool name the version was collected for"},
-                    },
+                    {"${task.process}": {"type": "string", "description": "The name of the process"}},
+                    {f"{self.component}": {"type": "string", "description": "The name of the tool"}},
                     {
-                        "version": {"type": "string", "description": "The version of the tool"},
+                        f"{self.component} --version": {
+                            "type": "eval",
+                            "description": "The expression to obtain the version of the tool",
+                        },
                     },
                 ]
             ]

diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
@@ -52,6 +52,7 @@ def __init__(
         self.failed: list[tuple[str, str, str, Path]] = []
         self.inputs: list[list[dict[str, dict[str, str]]]] = []
         self.outputs: list[str] = []
+        self.topics: dict[str, list[dict[str, dict] | list[dict[str, dict[str, str]]]]]
         self.has_meta: bool = False
         self.git_sha: str | None = None
         self.is_patched: bool = False
@@ -322,14 +323,18 @@ def get_topics_from_main_nf(self) -> None:
                 if topic_name in topics:
                     continue
                 topics[match_topic.group(1)] = []
-                for count, match_element in enumerate(matches_elements, start=1):
-                    output_val = None
+                for _, match_element in enumerate(matches_elements, start=1):
+                    topic_val = None
                     if match_element.group(3):
-                        output_val = match_element.group(3)
+                        topic_val = match_element.group(3)
                     elif match_element.group(4):
-                        output_val = match_element.group(4)
-                    if output_val:
-                        channel_elements.append({f"value{count}": {}})
+                        topic_val = match_element.group(4)
+                    if topic_val:
+                        topic_val = re.split(r',(?=(?:[^\'"]*[\'"][^\'"]*[\'"])*[^\'"]*$)', topic_val)[
+                            0
+                        ]  # Takes only first part, avoid commas in quotes
+                        topic_val = topic_val.strip().strip("'").strip('"')  # remove quotes and whitespaces
+                        channel_elements.append({topic_val: {}})
                 if len(channel_elements) == 1:
                     topics[match_topic.group(1)].append(channel_elements[0])
                 elif len(channel_elements) > 1:

diff --git a/nf_core/module-template/meta.yml b/nf_core/module-template/meta.yml
@@ -54,20 +54,20 @@ output:
           type: string
           description: The name of the tool
       - "{{ component }} --version":
-          type: string
-          description: The version of the tool
+          type: eval
+          description: The expression to obtain the version of the tool
 
 topics:
   versions:
-    - - process:
-          type: string
-          description: The process the versions were collected from
-      - tool:
+    - - "${task.process}":
           type: string
-          description: The tool name the version was collected for
-      - version:
+          description: The name of the process
+      - "{{ component }}":
           type: string
-          description: The version of the tool
+          description: The name of the tool
+      - "{{ component }} --version":
+          type: eval
+          description: The expression to obtain the version of the tool
 
 authors:
   - "{{ author }}"

diff --git a/nf_core/modules/lint/__init__.py b/nf_core/modules/lint/__init__.py
@@ -27,7 +27,7 @@
 
 from .environment_yml import environment_yml
 from .main_nf import main_nf
-from .meta_yml import meta_yml, obtain_inputs, obtain_outputs, read_meta_yml
+from .meta_yml import meta_yml, obtain_inputs, obtain_outputs, obtain_topics, read_meta_yml
 from .module_changes import module_changes
 from .module_deprecations import module_deprecations
 from .module_patch import module_patch
@@ -48,6 +48,7 @@ class ModuleLint(ComponentLint):
     meta_yml = meta_yml
     obtain_inputs = obtain_inputs
     obtain_outputs = obtain_outputs
+    obtain_topics = obtain_topics
     read_meta_yml = read_meta_yml
     module_changes = module_changes
     module_deprecations = module_deprecations
@@ -302,6 +303,8 @@ def update_meta_yml_file(self, mod):
         if "output" in meta_yml:
             correct_outputs = self.obtain_outputs(mod.outputs)
             meta_outputs = self.obtain_outputs(meta_yml["output"])
+            correct_topics = self.obtain_topics(mod.topics)
+            meta_topics = self.obtain_topics(meta_yml["topics"])
 
         def _find_meta_info(meta_yml, element_name, is_output=False) -> dict:
             """Find the information specified in the meta.yml file to update the corrected meta.yml content"""
@@ -367,6 +370,24 @@ def _find_meta_info(meta_yml, element_name, is_output=False) -> dict:
                         corrected_meta_yml["output"][ch_name][i][element_name] = _find_meta_info(
                             meta_yml["output"], element_name, is_output=True
                         )
+        elif "topics" in meta_yml and correct_topics != meta_topics:
+            log.debug(
+                f"Correct topics: '{correct_topics}' differ from current topics: '{meta_topics}' in '{mod.meta_yml}'"
+            )
+            corrected_meta_yml["topics"] = mod.topics.copy()
+            for t_name in corrected_meta_yml["topics"].keys():
+                for i, t_content in enumerate(corrected_meta_yml["topics"][t_name]):
+                    if isinstance(t_content, list):
+                        for j, element in enumerate(t_content):
+                            element_name = list(element.keys())[0]
+                            corrected_meta_yml["topics"][t_name][i][j][element_name] = _find_meta_info(
+                                meta_yml["topics"], element_name, is_output=True
+                            )
+                    elif isinstance(t_content, dict):
+                        element_name = list(t_content.keys())[0]
+                        corrected_meta_yml["topics"][t_name][i][element_name] = _find_meta_info(
+                            meta_yml["topics"], element_name, is_output=True
+                        )
 
         def _add_edam_ontologies(section, edam_formats, desc):
             expected_ontologies = []

diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
@@ -211,6 +211,29 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_m
                         module.meta_yml,
                     )
                 )
+        # Check that all topics are correctly specified
+        if "topics" in meta_yaml:
+            correct_topics = obtain_topics(module_lint_object, module.topics)
+            meta_topics = obtain_topics(module_lint_object, meta_yaml["topics"])
+
+            if correct_topics == meta_topics:
+                module.passed.append(
+                    (
+                        "meta_yml",
+                        "correct_meta_topics",
+                        "Correct topics specified in module `meta.yml`",
+                        module.meta_yml,
+                    )
+                )
+            else:
+                module.failed.append(
+                    (
+                        "meta_yml",
+                        "correct_meta_topics",
+                        f"Module `meta.yml` does not match `main.nf`. Topics should contain: {correct_topics}\nRun `nf-core modules lint --fix` to update the `meta.yml` file.",
+                        module.meta_yml,
+                    )
+                )
 
 
 def read_meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> dict | None:
@@ -301,3 +324,29 @@ def obtain_outputs(_, outputs: dict | list) -> dict | list:
         return [{k: v} for k, v in formatted_outputs.items()]
     else:
         return formatted_outputs
+
+
+def obtain_topics(_, topics: dict) -> dict:
+    """
+    Obtain the dictionary of topics and elements of each topic.
+
+    Args:
+        topics (dict): The dictionary of topics from main.nf or meta.yml files.
+
+    Returns:
+        formatted_topics (dict): A dictionary containing the topics and their elements obtained from main.nf or meta.yml files.
+    """
+    formatted_topics: dict = {}
+    for name in topics.keys():
+        content = topics[name]
+        t_elements: list = []
+        for element in content:
+            if isinstance(element, list):
+                t_elements.append([])
+                for e in element:
+                    t_elements[-1].append(list(e.keys())[0])
+            else:
+                t_elements.append(list(element.keys())[0])
+        formatted_topics[name] = t_elements
+
+    return formatted_topics