Merge branch 'feat/linting-nf-schema' of github.com:nvnieuwk/tools in…

…to feat/linting-nf-schema

nf_core/pipelines/create/templatefeatures.yml

@@ -262,7 +262,7 @@ nf_schema:
   short_description: "Use nf-schema"
   description: "Use the nf-schema Nextflow plugin for this pipeline."
   help_text: |
-    nf-schema is used to validate input parameters based on a JSON schema.
+    [nf-schema](https://nextflow-io.github.io/nf-schema/latest/) is used to validate input parameters based on a JSON schema.
     It also provides helper functionality to create help messages, get a summary
     of changed parameters and validate and convert a samplesheet to a channel.
   nfcore_pipelines: True

nf_core/pipelines/lint/plugin_includes.py

@@ -16,10 +16,10 @@ def plugin_includes(self) -> Dict[str, List[str]]:
     config_plugins = [plugin.split("@")[0] for plugin in ast.literal_eval(self.nf_config.get("plugins", "[]"))]
     validation_plugin = "nf-validation" if "nf-validation" in config_plugins else "nf-schema"
 
-    passed: list[str] = []
-    warned: list[str] = []
-    failed: list[str] = []
-    ignored: list[str] = []
+    passed: List[str] = []
+    warned: List[str] = []
+    failed: List[str] = []
+    ignored: List[str] = []
 
     plugin_include_pattern = re.compile(r"^include\s*{[^}]+}\s*from\s*[\"']plugin/([^\"']+)[\"']\s*$", re.MULTILINE)
     workflow_files = [