diff --git a/CHANGELOG.md b/CHANGELOG.md
index 57a4cff8ea..1d190fe85d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@
 - Add an empty line to `modules.json`, `params.json` and `nextflow-schema.json` when dumping them to avoid prettier errors.
 - Add actions workflow to respond to `@nf-core-bot fix linting` comments on nf-core/tools PRs
 - Linting: Don't allow a `.nf-core.yaml` file, should be `.yml` ([#1515](https://github.com/nf-core/tools/pull/1515)).
+- Not all definitions in JSON schema have a "properties", leading to an error ([#1419](https://github.com/nf-core/tools/issues/1419))
 
 ### Modules
 
diff --git a/nf_core/schema.py b/nf_core/schema.py
index 5784645543..522f48d20b 100644
--- a/nf_core/schema.py
+++ b/nf_core/schema.py
@@ -613,6 +613,29 @@ def get_wf_params(self):
                 )
             )
 
+    def remove_schema_empty_definitions(self):
+        """
+        Go through top-level schema remove definitions that don't have
+        any property attributes
+        """
+        # Make copy of schema
+        schema_no_empty_definitions = copy.deepcopy(self.schema)
+
+        ## Identify and remove empty definitions from the schema
+        empty_definitions = []
+        for d_key, d_schema in list(schema_no_empty_definitions.get("definitions", {}).items()):
+            if not d_schema['properties']:
+                del schema_no_empty_definitions["definitions"][d_key]
+                empty_definitions.append(d_key)
+
+        # Remove "allOf" group with empty definitions from the schema
+        for d_key in empty_definitions:
+            allOf = {'$ref': "#/definitions/{}".format(d_key)}
+            if allOf in schema_no_empty_definitions["allOf"]:
+                schema_no_empty_definitions["allOf"].remove(allOf)
+
+        self.schema = schema_no_empty_definitions
+
     def remove_schema_notfound_configs(self):
         """
         Go through top-level schema and all definitions sub-schemas to remove
@@ -625,6 +648,8 @@ def remove_schema_notfound_configs(self):
             cleaned_schema, p_removed = self.remove_schema_notfound_configs_single_schema(definition)
             self.schema["definitions"][d_key] = cleaned_schema
             params_removed.extend(p_removed)
+        self.remove_schema_empty_definitions()
+
         return params_removed
 
     def remove_schema_notfound_configs_single_schema(self, schema):