Merge branch 'dev' into version-badges

nf-core · Feb 12, 2025 · e411c65 · e411c65
2 parents 191d211 + 38813b0
commit e411c65
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diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.5
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -10,16 +10,16 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.3.3
+          - prettier@3.5.0
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.0.3"
+    rev: "3.1.2"
     hooks:
       - id: editorconfig-checker
         alias: ec
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.14.1"
+    rev: "v1.15.0"
     hooks:
       - id: mypy
         additional_dependencies:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,19 +1,52 @@
 # nf-core/tools: Changelog
 
-## v3.2.0dev
+## v3.3.0dev
 
 ### Template
 
+- Remove the on `pull_request_target` trigger and `pull_request` types from the download test. Also drop `push` triggers on other CI tests. ([#3399](https://github.com/nf-core/tools/pull/3399))
 - Add nf-core template version badges to README ([#3396](https://github.com/nf-core/tools/pull/3396))
 
 ### Linting
 
+- Add linting for ifEmpty(null) ([#3411](https://github.com/nf-core/tools/pull/3411))
+
 ### Modules
 
 ### Subworkflows
 
 ### General
 
+- output passed to write_params_file as Path object ([#3435](https://github.com/nf-core/tools/pull/3435))
+- chore(deps): update python:3.12-slim docker digest to 69ce3ae ([#3433](https://github.com/nf-core/tools/pull/3433))
+- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.4 ([#3438](https://github.com/nf-core/tools/pull/3438))
+- format name/value with YAML syntax ([#3442](https://github.com/nf-core/tools/pull/3442))
+- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.5 ([#3445](https://github.com/nf-core/tools/pull/3445))
+- chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.15.0 ([#3447](https://github.com/nf-core/tools/pull/3447))
+- Update prettier to 3.5.0 ([#3448](https://github.com/nf-core/tools/pull/3448))
+- chore(deps): update python:3.12-slim docker digest to 34656cd ([#3450](https://github.com/nf-core/tools/pull/3450))
+
+## [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

diff --git a/Dockerfile b/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:10f3aaab98db50cba827d3b33a91f39dc9ec2d02ca9b85cbc5008220d07b17f3
+FROM python:3.12-slim@sha256:34656cd90456349040784165b9decccbcee4de66f3ead0a1168ba893455afd1e
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for nf-core/tools"
 

diff --git a/docs/api/_src/pipeline_lint_tests/index.md b/docs/api/_src/pipeline_lint_tests/index.md
@@ -17,6 +17,7 @@
     - [nfcore_yml](./nfcore_yml/)
     - [pipeline_name_conventions](./pipeline_name_conventions/)
     - [pipeline_todos](./pipeline_todos/)
+    - [pipeline_if_empty_null](./pipeline_if_empty_null/)
     - [plugin_includes](./plugin_includes/)
     - [readme](./readme/)
     - [schema_description](./schema_description/)

diff --git a/docs/api/_src/pipeline_lint_tests/local_component_structure.md b/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
+```
diff --git a/docs/api/_src/pipeline_lint_tests/pipeline_if_empty_null.md b/docs/api/_src/pipeline_lint_tests/pipeline_if_empty_null.md
@@ -0,0 +1,5 @@
+# pipeline_if_empty_null
+
+```{eval-rst}
+.. automethod:: nf_core.pipelines.lint.PipelineLint.pipeline_if_empty_null
+```
diff --git a/docs/api/_src/subworkflow_lint_tests/index.md b/docs/api/_src/subworkflow_lint_tests/index.md
@@ -5,4 +5,5 @@
     - [subworkflow_changes](./subworkflow_changes/)
     - [subworkflow_tests](./subworkflow_tests/)
     - [subworkflow_todos](./subworkflow_todos/)
+    - [subworkflow_if_empty_null](./subworkflow_if_empty_null/)
     - [subworkflow_version](./subworkflow_version/)
diff --git a/docs/api/_src/subworkflow_lint_tests/subworkflow_if_empty_null.md b/docs/api/_src/subworkflow_lint_tests/subworkflow_if_empty_null.md
@@ -0,0 +1,5 @@
+# subworkflow_if_empty_null
+
+```{eval-rst}
+.. automethod:: nf_core.subworkflows.lint.SubworkflowLint.subworkflow_if_empty_null
+```
diff --git a/nf_core/commands_pipelines.py b/nf_core/commands_pipelines.py
@@ -218,7 +218,7 @@ def pipelines_create_params_file(ctx, pipeline, revision, output, force, show_hi
     """
     builder = ParamsFileBuilder(pipeline, revision)
 
-    if not builder.write_params_file(output, show_hidden=show_hidden, force=force):
+    if not builder.write_params_file(Path(output), show_hidden=show_hidden, force=force):
         sys.exit(1)
 
 

diff --git a/nf_core/components/components_command.py b/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"
         ]
 

diff --git a/nf_core/components/components_differ.py b/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)}'")

diff --git a/nf_core/components/create.py b/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
 

diff --git a/nf_core/components/info.py b/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"
                 )
             )

diff --git a/nf_core/components/lint/__init__.py b/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:
@@ -181,9 +185,16 @@ def get_all_module_lint_tests(is_pipeline):
     @staticmethod
     def get_all_subworkflow_lint_tests(is_pipeline):
         if is_pipeline:
-            return ["main_nf", "meta_yml", "subworkflow_changes", "subworkflow_todos", "subworkflow_version"]
+            return [
+                "main_nf",
+                "meta_yml",
+                "subworkflow_changes",
+                "subworkflow_todos",
+                "subworkflow_if_empty_null",
+                "subworkflow_version",
+            ]
         else:
-            return ["main_nf", "meta_yml", "subworkflow_todos", "subworkflow_tests"]
+            return ["main_nf", "meta_yml", "subworkflow_todos", "subworkflow_if_empty_null", "subworkflow_tests"]
 
     def set_up_pipeline_files(self):
         self.load_lint_config()

diff --git a/nf_core/components/nfcore_component.py b/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()
 

diff --git a/nf_core/components/remove.py b/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