Document ext.args in meta yml

nf_core/components/info.py

@@ -240,6 +240,12 @@ def generate_params_table(self, type) -> Table:
             table.add_column("Structure", justify="right", style="green")
         return table
 
+    def generate_args_table(self) -> Table:
+        table = Table(expand=True, show_lines=True, box=box.MINIMAL_HEAVY_HEAD, padding=0)
+        table.add_column(":hammer_and_wrench:  Extra Args")
+        table.add_column("Description")
+        return table
+
     def get_channel_structure(self, structure: dict) -> str:
         "Get the structure of a channel"
         structure_str = ""
@@ -341,6 +347,17 @@ def generate_component_info_help(self):
 
             renderables.append(outputs_table)
 
+        # args
+        if self.meta.get("args"):
+            args_table = self.generate_args_table()
+            for argname, arginfo in self.meta["args"].items():
+                args_table.add_row(
+                    f"[orange1 on black] {argname} [/][dim i]",
+                    Markdown(arginfo["description"] if arginfo["description"] else ""),
+                )
+
+            renderables.append(args_table)
+
         # Installation command
         if self.remote_location and not self.local:
             cmd_base = f"nf-core {self.component_type}"

nf_core/components/nfcore_component.py

@@ -279,3 +279,24 @@ def get_outputs_from_main_nf(self):
                     pass
             log.debug(f"Found {len(outputs)} outputs in {self.main_nf}")
             self.outputs = outputs
+
+    def get_ext_args_from_main_nf(self) -> List[str]:
+        """Collect all ext.args from the main.nf file."""
+        if self.component_type == "modules":
+            extargs: set[str] = set()
+            with open(self.main_nf) as f:
+                data = f.read()
+                section_identifier = "script:"
+                if "script:" not in data:
+                    section_identifier = "exec:"
+                    if "exec:" not in data:
+                        log.debug(f"Could not find 'script' or 'exec' section in {self.main_nf}")
+                        return []
+                input_data = data.split(section_identifier)[1].split("stub:")[0]
+                regex = r"ext.(args[0-9]*) "
+                matches = re.finditer(regex, input_data)
+                for m in matches:
+                    extargs.add(m.group(1))
+                log.debug(f"Found {len(extargs)} extra args in {self.main_nf}")
+            return sorted(extargs)
+        return []

nf_core/module-template/meta.yml

@@ -22,6 +22,13 @@ tools:
       licence: {{ tool_licence }}
       identifier: {{ tool_identifier }}
 
+{% if not_empty_template -%}
+## TODO nf-core: Add a description of all of the ext.args used in the pipeline
+{% endif -%}
+extra_args:
+  args:
+    description: "{{ component }}"
+
 {% if not_empty_template -%}
 ## TODO nf-core: Add a description of all of the variables used as input
 {% endif -%}

nf_core/modules/lint/meta_yml.py

@@ -50,7 +50,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_m
             return
         raise LintExceptionError("Module does not have a `meta.yml` file")
     # Check if we have a patch file, get original file in that case
-    meta_yaml = read_meta_yml(module_lint_object, module)
+    meta_yaml_content = read_meta_yml(module_lint_object, module)
     if module.is_patched and module_lint_object.modules_repo.repo_path is not None:
         lines = ComponentsDiffer.try_apply_patch(
             module.component_type,
@@ -62,8 +62,8 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_m
         ).get("meta.yml")
         if lines is not None:
             yaml = ruamel.yaml.YAML()
-            meta_yaml = yaml.load("".join(lines))
-    if meta_yaml is None:
+            meta_yaml_content = yaml.load("".join(lines))
+    if meta_yaml_content is None:
         module.failed.append(("meta_yml_exists", "Module `meta.yml` does not exist", module.meta_yml))
         return
     else:
@@ -74,7 +74,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_m
     try:
         with open(Path(module_lint_object.modules_repo.local_repo_dir, "modules/meta-schema.json")) as fh:
             schema = json.load(fh)
-        validators.validate(instance=meta_yaml, schema=schema)
+        validators.validate(instance=meta_yaml_content, schema=schema)
         module.passed.append(("meta_yml_valid", "Module `meta.yml` is valid", module.meta_yml))
         valid_meta_yml = True
     except exceptions.ValidationError as e:
@@ -85,7 +85,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_m
             hint = f"\nCheck that the child entries of {str(e.path[0]) + '.' + str(e.path[2])} are indented correctly."
         if e.schema and isinstance(e.schema, dict) and "message" in e.schema:
             e.message = e.schema["message"]
-            incorrect_value = meta_yaml
+            incorrect_value = meta_yaml_content
             for key in e.path:
                 incorrect_value = incorrect_value[key]
 
@@ -101,7 +101,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_m
     # Confirm that all input and output channels are correctly specified
     if valid_meta_yml:
         # confirm that the name matches the process name in main.nf
-        if meta_yaml["name"].upper() == module.process_name:
+        if meta_yaml_content["name"].upper() == module.process_name:
             module.passed.append(
                 (
                     "meta_name",
@@ -113,12 +113,12 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_m
             module.failed.append(
                 (
                     "meta_name",
-                    f"Conflicting `process` name between meta.yml (`{meta_yaml['name']}`) and main.nf (`{module.process_name}`)",
+                    f"Conflicting `process` name between meta.yml (`{meta_yaml_content['name']}`) and main.nf (`{module.process_name}`)",
                     module.meta_yml,
                 )
             )
         # Check that inputs are specified in meta.yml
-        if len(module.inputs) > 0 and "input" not in meta_yaml:
+        if len(module.inputs) > 0 and "input" not in meta_yaml_content:
             module.failed.append(
                 (
                     "meta_input",
@@ -137,8 +137,10 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_m
         else:
             log.debug(f"No inputs specified in module `main.nf`: {module.component_name}")
         # Check that all inputs are correctly specified
-        if "input" in meta_yaml:
-            correct_inputs, meta_inputs = obtain_correct_and_specified_inputs(module_lint_object, module, meta_yaml)
+        if "input" in meta_yaml_content:
+            correct_inputs, meta_inputs = obtain_correct_and_specified_inputs(
+                module_lint_object, module, meta_yaml_content
+            )
 
             if correct_inputs == meta_inputs:
                 module.passed.append(
@@ -158,7 +160,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_m
                 )
 
         # Check that outputs are specified in meta.yml
-        if len(module.outputs) > 0 and "output" not in meta_yaml:
+        if len(module.outputs) > 0 and "output" not in meta_yaml_content:
             module.failed.append(
                 (
                     "meta_output",
@@ -175,8 +177,10 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_m
                 )
             )
         # Check that all outputs are correctly specified
-        if "output" in meta_yaml:
-            correct_outputs, meta_outputs = obtain_correct_and_specified_outputs(module_lint_object, module, meta_yaml)
+        if "output" in meta_yaml_content:
+            correct_outputs, meta_outputs = obtain_correct_and_specified_outputs(
+                module_lint_object, module, meta_yaml_content
+            )
 
             if correct_outputs == meta_outputs:
                 module.passed.append(
@@ -195,6 +199,26 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_m
                     )
                 )
 
+        # Check that ext.args are listed in the `extra_args` section
+        expected_extra_args = module.get_ext_args_from_main_nf()
+        extra_args_yml = sorted(meta_yaml_content.get("extra_args", {}).keys())
+        if expected_extra_args == extra_args_yml:
+            module.passed.append(
+                (
+                    "correct_extra_args",
+                    "Correct extra args specified in `meta.yml`",
+                    module.meta_yml,
+                )
+            )
+        else:
+            module.warned.append(
+                (
+                    "correct_extra_args",
+                    f"Module `meta.yml` does not match `main.nf`. Extra args should contain: {extra_args_yml}\n",
+                    module.meta_yml,
+                )
+            )
+
 
 def read_meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> Union[dict, None]:
     """