fix docstrings

Author: mashehu

nf_core/components/info.py

@@ -173,7 +173,7 @@ def get_local_yaml(self) -> dict | None:
         """Attempt to get the meta.yml file from a locally installed module/subworkflow.
 
         Returns:
-            Optional[dict]: Parsed meta.yml if found, None otherwise
+            dict | None: Parsed meta.yml if found, None otherwise
         """
 
         if self.repo_type == "pipeline":

nf_core/modules/lint/main_nf.py

@@ -249,7 +249,7 @@ def check_process_section(self, lines, registry, fix_version, progress_bar):
         progress_bar (ProgressBar): Progress bar to update.
 
     Returns:
-        Optional[bool]: True if singularity and docker containers match, False otherwise. If process definition does not exist, None.
+        bool | None: True if singularity and docker containers match, False otherwise. If process definition does not exist, None.
     """
     # Check that we have a process section
     if len(lines) == 0:

nf_core/pipelines/bump_version.py

@@ -210,7 +210,7 @@ def update_file_version(
         patterns (List[Tuple[str, str]]): A list of tuples containing the regex patterns to
             match and the replacement strings.
         required (bool, optional): Whether the file is required to exist. Defaults to `True`.
-        yaml_key (Optional[List[str]], optional): The YAML key to update. Defaults to `None`.
+        yaml_key (List[str] | None, optional): The YAML key to update. Defaults to `None`.
     """
     fn: Path = pipeline_obj._fp(filename)
 

nf_core/pipelines/download/container_fetcher.py

@@ -190,8 +190,8 @@ class ContainerFetcher(ABC):
         container_library (Iterable[str]): A collection of container libraries to use
         registry_set (Iterable[str]): A collection of registries to consider
         progress_factory (Callable[[], ContainerProgress]): A factory to create a progress bar.
-        library_dir (Optional[Path]): The directory to look for container images in.
-        cache_dir (Optional[Path]): A directory where container images might be cached.
+        library_dir (Path | None): The directory to look for container images in.
+        cache_dir (Path | None): A directory where container images might be cached.
         amend_cachedir (bool): Whether to amend the cache directory with the container images.
         parallel (int): The number of containers to fetch in parallel.
     """

nf_core/pipelines/download/download.py

@@ -47,18 +47,18 @@ class DownloadWorkflow:
     Can also download its Singularity container image if required.
 
     Args:
-        pipeline (Optional[str]): A nf-core pipeline name.
-        revision (Optional[Union[tuple[str], str]]): The workflow revision(s) to download, like `1.0` or `dev` . Defaults to None.
-        outdir (Optional[Path]): Path to the local download directory. Defaults to None.
-        compress_type (Optional[str]): Type of compression for the downloaded files. Defaults to None.
+        pipeline (str | None): A nf-core pipeline name.
+        revision (tuple[str] | str | None): The workflow revision(s) to download, like `1.0` or `dev` . Defaults to None.
+        outdir (Path | None): Path to the local download directory. Defaults to None.
+        compress_type (str | None): Type of compression for the downloaded files. Defaults to None.
         force (bool): Flag to force download even if files already exist (overwrite existing files). Defaults to False.
         platform (bool): Flag to customize the download for Seqera Platform (convert to git bare repo). Defaults to False.
-        download_configuration (Optional[str]): Download the configuration files from nf-core/configs. Defaults to None.
-        additional_tags (Optional[Union[list[str], str]]): Specify additional tags to add to the downloaded pipeline. Defaults to None.
+        download_configuration (str | None): Download the configuration files from nf-core/configs. Defaults to None.
+        additional_tags (list[str] | str | None): Specify additional tags to add to the downloaded pipeline. Defaults to None.
         container_system (str): The container system to use (e.g., "singularity"). Defaults to None.
-        container_library (Optional[Union[tuple[str], str]]): The container libraries (registries) to use. Defaults to None.
-        container_cache_utilisation (Optional[str]): If a local or remote cache of already existing container images should be considered. Defaults to None.
-        container_cache_index (Optional[Path]): An index for the remote container cache. Defaults to None.
+        container_library (tuple[str] | str | None): The container libraries (registries) to use. Defaults to None.
+        container_cache_utilisation (str | None): If a local or remote cache of already existing container images should be considered. Defaults to None.
+        container_cache_index (Path | None): An index for the remote container cache. Defaults to None.
         parallel (int): The number of parallel downloads to use. Defaults to 4.
         hide_progress (bool): Flag to hide the progress bar. Defaults to False.
     """