nf-core · ewels · May 5, 2021 · May 3, 2021 · May 3, 2021 · May 3, 2021
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,8 +17,9 @@
 * Merge markers lint test - ignore binary files, allow config to ignore specific files [[#1040](https://github.com/nf-core/tools/pull/1040)]
 * New lint test to check if params in `nextflow config` are mentioned in `main.nf` [[#1038](https://github.com/nf-core/tools/issues/1038)]
 * New modules lint test comparing the `functions.nf` file to the template version
+* Added lint checks for missing parameter description and parameters outside of groups [[#1017](https://github.com/nf-core/tools/issues/1017)]
+* Added fix to remove warnings about params that get converted from camelCase to camel-case [[#1035](https://github.com/nf-core/tools/issues/1035)]
 * Use latest stable Nextflow version `21.04.0` for CI tests instead of the `-edge` release
-* Added temporary fix to remove warnings about params that get converted from camelCase to camel-case [[#1035](https://github.com/nf-core/tools/issues/1035)]
 * Fix bug in `nf-core download` where image names were getting a hyphen in `nf-core` which was breaking things.
 
 ### Template

diff --git a/docs/api/_src/pipeline_lint_tests/schema_description.rst b/docs/api/_src/pipeline_lint_tests/schema_description.rst
@@ -0,0 +1,4 @@
+schema_description
+===========
+
+.. automethod:: nf_core.lint.PipelineLint.schema_description
diff --git a/nf_core/lint/__init__.py b/nf_core/lint/__init__.py
@@ -113,6 +113,7 @@ class PipelineLint(nf_core.utils.Pipeline):
     from .readme import readme
     from .schema_lint import schema_lint
     from .schema_params import schema_params
+    from .schema_description import schema_description
     from .template_strings import template_strings
     from .version_consistency import version_consistency
 
@@ -147,6 +148,7 @@ def __init__(self, wf_path, release_mode=False, fix=(), key=(), fail_ignored=Fal
             "template_strings",
             "schema_lint",
             "schema_params",
+            "schema_description",
             "actions_schema_validation",
             "merge_markers",
         ]

diff --git a/nf_core/lint/schema_description.py b/nf_core/lint/schema_description.py
@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+
+from logging import warn
+import nf_core.schema
+
+
+def schema_description(self):
+    """Check that every parameter in the schema has a description
+
+    The ``nextflow_schema.json`` pipeline schema should describe every flat parameter
+    Furthermore warns about parameters outside of groups
+
+    * Warning: Parameters in ``nextflow_schema.json`` without a description
+    * Warning: Parameters in ``nextflow_schema.json`` that are defined outside of a group
+    """
+    passed = []
+    warned = []
+    ignored = []
+
+    # First, get the top-level config options for the pipeline
+    # Schema object already created in the `schema_lint` test
+    self.schema_obj = nf_core.schema.PipelineSchema()
+    self.schema_obj.get_schema_path(self.wf_path)
+    self.schema_obj.get_wf_params()
+    self.schema_obj.no_prompts = True
+    self.schema_obj.load_lint_schema()
+
+    # Get parameters that should be ignored according to the linting config
+    ignore_params = self.lint_config.get("schema_description", [])
+
+    # Get ungrouped params
+    if "properties" in self.schema_obj.schema.keys():
+        ungrouped_params = self.schema_obj.schema["properties"].keys()
+        for up in ungrouped_params:
+            if up in ignore_params:
+                ignored.append(f"Ignored ungrouped param in schema: `{up}`")
+            else:
+                warned.append(f"Ungrouped param in schema: `{up}`")
+
+    # Iterate over groups and add warning for parameters without a description
+    for group_key in self.schema_obj.schema["definitions"].keys():
+        group = self.schema_obj.schema["definitions"][group_key]
+        for param_key, param in group["properties"].items():
+            if param_key in ignore_params:
+                ignored.append(f"Ignoring description check for param in schema: `{param_key}`")
+                continue
+            if "description" not in param.keys():
+                warned.append(f"No description provided in schema for parameter: `{param_key}`")
+
+    for ip in ignore_params:
+        ignored.append(f"Parameter is ignored: `{ip}`")
+
+    return {"passed": passed, "warned": warned, "ignored": ignored}
diff --git a/nf_core/lint/schema_params.py b/nf_core/lint/schema_params.py
@@ -17,10 +17,11 @@ def schema_params(self):
     failed = []
 
     # First, get the top-level config options for the pipeline
-    # Schema object already created in the `schema_lint` test
+    self.schema_obj = nf_core.schema.PipelineSchema()
     self.schema_obj.get_schema_path(self.wf_path)
     self.schema_obj.get_wf_params()
     self.schema_obj.no_prompts = True
+    self.schema_obj.load_lint_schema()
 
     # Remove any schema params not found in the config
     removed_params = self.schema_obj.remove_schema_notfound_configs()