Merge pull request #3428 from nf-core/dev

dev -> main for 3.2.0 release

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.3
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -13,7 +13,7 @@ repos:
           - [email protected]
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.0.3"
+    rev: "3.1.2"
     hooks:
       - id: editorconfig-checker
         alias: ec

CHANGELOG.md

@@ -1,5 +1,26 @@
 # nf-core/tools: Changelog
 
+## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]
+
+### Template
+
+- Remove automated release tweets ([#3419](https://github.com/nf-core/tools/pull/3419))
+- Update template components ([#3426](https://github.com/nf-core/tools/pull/3426))
+- Fix `process.shell` in `nextflow.config` ([#3416](https://github.com/nf-core/tools/pull/3416)) and split into new lines ([#3425](https://github.com/nf-core/tools/pull/3425))
+
+### Modules
+
+- Modules created in pipelines "local" dir now use the full template ([#3256](https://github.com/nf-core/tools/pull/3256))
+
+### Subworkflows
+
+- Subworkflows created in pipelines "local" dir now use the full template ([#3256](https://github.com/nf-core/tools/pull/3256))
+
+### General
+
+- Update pre-commit hook editorconfig-checker/editorconfig-checker.python to v3.1.2 ([#3414](https://github.com/nf-core/tools/pull/3414))
+- Update python:3.12-slim Docker digest to 123be56 ([#3421](https://github.com/nf-core/tools/pull/3421))
+
 ## [v3.1.2 - Brass Boxfish Patch](https://github.com/nf-core/tools/releases/tag/3.1.2) - [2025-01-20]
 
 ### Template

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:10f3aaab98db50cba827d3b33a91f39dc9ec2d02ca9b85cbc5008220d07b17f3
+FROM python:3.12-slim@sha256:123be5684f39d8476e64f47a5fddf38f5e9d839baff5c023c815ae5bdfae0df7
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for nf-core/tools"
 

docs/api/_src/pipeline_lint_tests/local_component_structure.md

@@ -0,0 +1,5 @@
+# modules_structure
+
+```{eval-rst}
+.. automethod:: nf_core.pipelines.lint.PipelineLint.local_component_structure
+```

nf_core/components/components_command.py

@@ -71,6 +71,10 @@ def get_local_components(self) -> List[str]:
         """
         local_component_dir = Path(self.directory, self.component_type, "local")
         return [
+            str(Path(directory).relative_to(local_component_dir))
+            for directory, _, files in os.walk(local_component_dir)
+            if "main.nf" in files
+        ] + [
             str(path.relative_to(local_component_dir)) for path in local_component_dir.iterdir() if path.suffix == ".nf"
         ]
 

nf_core/components/components_differ.py

@@ -271,9 +271,7 @@ def print_diff(
         console = Console(force_terminal=nf_core.utils.rich_force_colors())
         if current_version is not None and new_version is not None:
             log.info(
-                f"Changes in component '{Path(repo_path, component)}' between"
-                f" ({current_version}) and"
-                f" ({new_version})"
+                f"Changes in component '{Path(repo_path, component)}' between ({current_version}) and ({new_version})"
             )
         else:
             log.info(f"Changes in component '{Path(repo_path, component)}'")

nf_core/components/create.py

@@ -75,11 +75,11 @@ def create(self) -> bool:
         e.g bam_sort or bam_sort_samtools, respectively.
 
         If <directory> is a pipeline, this function creates a file called:
-        '<directory>/modules/local/tool.nf'
+        '<directory>/modules/local/tool/main.nf'
             OR
-        '<directory>/modules/local/tool_subtool.nf'
+        '<directory>/modules/local/tool/subtool/main.nf'
             OR for subworkflows
-        '<directory>/subworkflows/local/subworkflow_name.nf'
+        '<directory>/subworkflows/local/subworkflow_name/main.nf'
 
         If <directory> is a clone of nf-core/modules, it creates or modifies the following files:
 
@@ -355,70 +355,46 @@ def _get_component_dirs(self) -> Dict[str, Path]:
         """
         file_paths = {}
         if self.repo_type == "pipeline":
-            local_component_dir = Path(self.directory, self.component_type, "local")
-            # Check whether component file already exists
-            component_file = local_component_dir / f"{self.component_name}.nf"
-            if component_file.exists() and not self.force_overwrite:
-                raise UserWarning(
-                    f"{self.component_type[:-1].title()} file exists already: '{component_file}'. Use '--force' to overwrite"
-                )
-
-            if self.component_type == "modules":
-                # If a subtool, check if there is a module called the base tool name already
-                if self.subtool and (local_component_dir / f"{self.component}.nf").exists():
-                    raise UserWarning(
-                        f"Module '{self.component}' exists already, cannot make subtool '{self.component_name}'"
-                    )
-
-                # If no subtool, check that there isn't already a tool/subtool
-                tool_glob = glob.glob(f"{local_component_dir}/{self.component}_*.nf")
-                if not self.subtool and tool_glob:
-                    raise UserWarning(
-                        f"Module subtool '{tool_glob[0]}' exists already, cannot make tool '{self.component_name}'"
-                    )
-
-            # Set file paths
-            file_paths["main.nf"] = component_file
+            component_dir = Path(self.directory, self.component_type, "local", self.component_dir)
 
         elif self.repo_type == "modules":
             component_dir = Path(self.directory, self.component_type, self.org, self.component_dir)
-            # Check if module/subworkflow directories exist already
-            if component_dir.exists() and not self.force_overwrite and not self.migrate_pytest:
-                raise UserWarning(
-                    f"{self.component_type[:-1]} directory exists: '{component_dir}'. Use '--force' to overwrite"
-                )
+        else:
+            raise ValueError("`repo_type` not set correctly")
 
-            if self.component_type == "modules":
-                # If a subtool, check if there is a module called the base tool name already
-                parent_tool_main_nf = Path(
-                    self.directory,
-                    self.component_type,
-                    self.org,
-                    self.component,
-                    "main.nf",
+        # Check if module/subworkflow directories exist already
+        if component_dir.exists() and not self.force_overwrite and not self.migrate_pytest:
+            raise UserWarning(
+                f"{self.component_type[:-1]} directory exists: '{component_dir}'. Use '--force' to overwrite"
+            )
+
+        if self.component_type == "modules":
+            # If a subtool, check if there is a module called the base tool name already
+            parent_tool_main_nf = Path(
+                self.directory,
+                self.component_type,
+                self.org,
+                self.component,
+                "main.nf",
+            )
+            if self.subtool and parent_tool_main_nf.exists() and not self.migrate_pytest:
+                raise UserWarning(
+                    f"Module '{parent_tool_main_nf}' exists already, cannot make subtool '{self.component_name}'"
                 )
-                if self.subtool and parent_tool_main_nf.exists() and not self.migrate_pytest:
-                    raise UserWarning(
-                        f"Module '{parent_tool_main_nf}' exists already, cannot make subtool '{self.component_name}'"
-                    )
 
-                # If no subtool, check that there isn't already a tool/subtool
-                tool_glob = glob.glob(
-                    f"{Path(self.directory, self.component_type, self.org, self.component)}/*/main.nf"
+            # If no subtool, check that there isn't already a tool/subtool
+            tool_glob = glob.glob(f"{Path(self.directory, self.component_type, self.org, self.component)}/*/main.nf")
+            if not self.subtool and tool_glob and not self.migrate_pytest:
+                raise UserWarning(
+                    f"Module subtool '{tool_glob[0]}' exists already, cannot make tool '{self.component_name}'"
                 )
-                if not self.subtool and tool_glob and not self.migrate_pytest:
-                    raise UserWarning(
-                        f"Module subtool '{tool_glob[0]}' exists already, cannot make tool '{self.component_name}'"
-                    )
-            # Set file paths
-            # For modules - can be tool/ or tool/subtool/ so can't do in template directory structure
-            file_paths["main.nf"] = component_dir / "main.nf"
-            file_paths["meta.yml"] = component_dir / "meta.yml"
-            if self.component_type == "modules":
-                file_paths["environment.yml"] = component_dir / "environment.yml"
-            file_paths["tests/main.nf.test.j2"] = component_dir / "tests" / "main.nf.test"
-        else:
-            raise ValueError("`repo_type` not set correctly")
+        # Set file paths
+        # For modules - can be tool/ or tool/subtool/ so can't do in template directory structure
+        file_paths["main.nf"] = component_dir / "main.nf"
+        file_paths["meta.yml"] = component_dir / "meta.yml"
+        if self.component_type == "modules":
+            file_paths["environment.yml"] = component_dir / "environment.yml"
+        file_paths["tests/main.nf.test.j2"] = component_dir / "tests" / "main.nf.test"
 
         return file_paths
 

nf_core/components/info.py

@@ -265,9 +265,9 @@ def generate_component_info_help(self):
             intro_text.append(
                 Text.from_markup(
                     ":globe_with_meridians: Repository: "
-                    f"{ '[link={self.remote_location}]' if self.remote_location.startswith('http') else ''}"
+                    f"{'[link={self.remote_location}]' if self.remote_location.startswith('http') else ''}"
                     f"{self.remote_location}"
-                    f"{'[/link]' if self.remote_location.startswith('http') else '' }"
+                    f"{'[/link]' if self.remote_location.startswith('http') else ''}"
                     "\n"
                 )
             )

nf_core/components/lint/__init__.py

@@ -102,7 +102,7 @@ def __init__(
                     continue
                 if isinstance(components, str):
                     raise LookupError(
-                        f"Error parsing modules.json: {components}. " f"Please check the file for errors or try again."
+                        f"Error parsing modules.json: {components}. Please check the file for errors or try again."
                     )
                 for org, comp in components:
                     self.all_remote_components.append(
@@ -162,6 +162,10 @@ def _set_registry(self, registry) -> None:
             self.registry = registry
         log.debug(f"Registry set to {self.registry}")
 
+    @property
+    def local_module_exclude_tests(self):
+        return ["module_version", "module_changes", "modules_patch"]
+
     @staticmethod
     def get_all_module_lint_tests(is_pipeline):
         if is_pipeline:

nf_core/components/nfcore_component.py

@@ -74,8 +74,8 @@ def __init__(
             repo_dir = self.component_dir.parts[:name_index][-1]
 
             self.org = repo_dir
-            self.nftest_testdir = Path(self.component_dir, "tests")
-            self.nftest_main_nf = Path(self.nftest_testdir, "main.nf.test")
+            self.nftest_testdir: Optional[Path] = Path(self.component_dir, "tests")
+            self.nftest_main_nf: Optional[Path] = Path(self.nftest_testdir, "main.nf.test")
 
             if self.repo_type == "pipeline":
                 patch_fn = f"{self.component_name.replace('/', '-')}.diff"
@@ -85,15 +85,23 @@ def __init__(
                     self.patch_path = patch_path
         else:
             # The main file is just the local module
-            self.main_nf = self.component_dir
-            self.component_name = self.component_dir.stem
-            # These attributes are only used by nf-core modules
-            # so just initialize them to None
-            self.meta_yml = None
-            self.environment_yml = None
-            self.test_dir = None
-            self.test_yml = None
-            self.test_main_nf = None
+            if self.component_dir.is_dir():
+                self.main_nf = Path(self.component_dir, "main.nf")
+                self.component_name = self.component_dir.stem
+                # These attributes are only required by nf-core modules
+                # so just set them to None if they don't exist
+                self.meta_yml = p if (p := Path(self.component_dir, "meta.yml")).exists() else None
+                self.environment_yml = p if (p := Path(self.component_dir, "environment.yml")).exists() else None
+                self.nftest_testdir = p if (p := Path(self.component_dir, "tests")).exists() else None
+                if self.nftest_testdir is not None:
+                    self.nftest_main_nf = p if (p := Path(self.nftest_testdir, "main.nf.test")).exists() else None
+            else:
+                self.main_nf = self.component_dir
+                self.component_dir = self.component_dir.parent
+                self.meta_yml = None
+                self.environment_yml = None
+                self.nftest_testdir = None
+                self.nftest_main_nf = None
 
         self.process_name: str = self._get_process_name()
 

nf_core/components/remove.py

@@ -176,6 +176,6 @@ def remove(self, component, removed_by=None, removed_components=None, force=Fals
                     f"Did not remove '{component}', because it was also manually installed. Only updated 'installed_by' entry in modules.json."
                 )
             log.info(
-                f"""Did not remove {self.component_type[:-1]} '{component}', because it was also installed by {', '.join(f"'{d}'" for d in installed_by)}. Only updated the 'installed_by' entry in modules.json."""
+                f"""Did not remove {self.component_type[:-1]} '{component}', because it was also installed by {", ".join(f"'{d}'" for d in installed_by)}. Only updated the 'installed_by' entry in modules.json."""
             )
         return removed

nf_core/modules/lint/__init__.py

@@ -117,7 +117,7 @@ def lint(
         """
         # TODO: consider unifying modules and subworkflows lint() function and add it to the ComponentLint class
         # Prompt for module or all
-        if module is None and not all_modules and len(self.all_remote_components) > 0:
+        if module is None and not (local or all_modules) and len(self.all_remote_components) > 0:
             questions = [
                 {
                     "type": "list",
@@ -170,7 +170,7 @@ def lint(
             self.lint_modules(local_modules, registry=registry, local=True, fix_version=fix_version)
 
         # Lint nf-core modules
-        if len(remote_modules) > 0:
+        if not local and len(remote_modules) > 0:
             self.lint_modules(remote_modules, registry=registry, local=False, fix_version=fix_version)
 
         if print_results:
@@ -234,7 +234,23 @@ def lint_module(
         # TODO: consider unifying modules and subworkflows lint_module() function and add it to the ComponentLint class
         # Only check the main script in case of a local module
         if local:
-            self.main_nf(mod, fix_version, self.registry, progress_bar)
+            mod.get_inputs_from_main_nf()
+            mod.get_outputs_from_main_nf()
+            # Update meta.yml file if requested
+            if self.fix and mod.meta_yml is not None:
+                self.update_meta_yml_file(mod)
+
+            for test_name in self.lint_tests:
+                if test_name in self.local_module_exclude_tests:
+                    continue
+                if test_name == "main_nf":
+                    getattr(self, test_name)(mod, fix_version, self.registry, progress_bar)
+                elif test_name in ["meta_yml", "environment_yml"]:
+                    # Allow files to be missing for local
+                    getattr(self, test_name)(mod, allow_missing=True)
+                else:
+                    getattr(self, test_name)(mod)
+
             self.passed += [LintResult(mod, *m) for m in mod.passed]
             warned = [LintResult(mod, *m) for m in (mod.warned + mod.failed)]
             if not self.fail_warned:

nf_core/modules/lint/environment_yml.py

@@ -12,7 +12,7 @@
 log = logging.getLogger(__name__)
 
 
-def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None:
+def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_missing: bool = False) -> None:
     """
     Lint an ``environment.yml`` file.
 
@@ -23,6 +23,15 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
     env_yml = None
     #  load the environment.yml file
     if module.environment_yml is None:
+        if allow_missing:
+            module.warned.append(
+                (
+                    "environment_yml_exists",
+                    "Module's `environment.yml` does not exist",
+                    Path(module.component_dir, "environment.yml"),
+                ),
+            )
+            return
         raise LintExceptionError("Module does not have an `environment.yml` file")
     try:
         with open(module.environment_yml) as fh:

nf_core/modules/lint/meta_yml.py

@@ -13,7 +13,7 @@
 log = logging.getLogger(__name__)
 
 
-def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None:
+def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent, allow_missing: bool = False) -> None:
     """
     Lint a ``meta.yml`` file
 
@@ -42,7 +42,13 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
         module (NFCoreComponent): The module to lint
 
     """
-
+    if module.meta_yml is None:
+        if allow_missing:
+            module.warned.append(
+                ("meta_yml_exists", "Module `meta.yml` does not exist", Path(module.component_dir, "meta.yml"))
+            )
+            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)
     if module.is_patched and module_lint_object.modules_repo.repo_path is not None:
@@ -56,9 +62,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
         ).get("meta.yml")
         if lines is not None:
             yaml = ruamel.yaml.YAML()
-            meta_yaml = yaml.safe_load("".join(lines))
-    if module.meta_yml is None:
-        raise LintExceptionError("Module does not have a `meta.yml` file")
+            meta_yaml = yaml.load("".join(lines))
     if meta_yaml is None:
         module.failed.append(("meta_yml_exists", "Module `meta.yml` does not exist", module.meta_yml))
         return
@@ -78,7 +82,7 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
         if len(e.path) > 0:
             hint = f"\nCheck the entry for `{e.path[0]}`."
         if e.message.startswith("None is not of type 'object'") and len(e.path) > 2:
-            hint = f"\nCheck that the child entries of {str(e.path[0])+'.'+str(e.path[2])} are indented correctly."
+            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