update JSON schema for modules meta.yml (#5837)

* update JSON schema for modules meta.yml * add identifier and ontologies to the modules meta.yml JSON schema * remove qualifier --------- Co-authored-by: Phil Ewels <[email protected]>
nf-core · Sep 19, 2024 · c9caefa · c9caefa
1 parent bb92ca2
commit c9caefa
Showing 1 changed file with 55 additions and 64 deletions.
diff --git a/modules/meta-schema.json b/modules/meta-schema.json
@@ -38,76 +38,14 @@
             "type": "array",
             "description": "Input channels for the module",
             "items": {
-                "type": "object",
-                "patternProperties": {
-                    ".*": {
-                        "type": "object",
-                        "properties": {
-                            "type": {
-                                "type": "string",
-                                "description": "Type of the input channel",
-                                "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"]
-                            },
-                            "description": {
-                                "type": "string",
-                                "description": "Description of the input channel"
-                            },
-                            "pattern": {
-                                "type": "string",
-                                "description": "Pattern of the input channel, given in Java glob syntax"
-                            },
-                            "default": {
-                                "type": ["string", "number", "boolean", "array", "object"],
-                                "description": "Default value for the input channel"
-                            },
-                            "enum": {
-                                "type": "array",
-                                "description": "List of allowed values for the input channel",
-                                "items": {
-                                    "type": ["string", "number", "boolean", "array", "object"]
-                                },
-                                "uniqueItems": true
-                            }
-                        },
-                        "required": ["type", "description"]
-                    }
-                }
+                "type": "array", "items": { "$ref": "#/definitions/elementProperties" }
             }
         },
         "output": {
             "type": "array",
             "description": "Output channels for the module",
             "items": {
-                "type": "object",
-                "patternProperties": {
-                    ".*": {
-                        "type": "object",
-                        "properties": {
-                            "type": {
-                                "type": "string",
-                                "description": "Type of the output channel",
-                                "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"]
-                            },
-                            "description": {
-                                "type": "string",
-                                "description": "Description of the output channel"
-                            },
-                            "pattern": {
-                                "type": "string",
-                                "description": "Pattern of the input channel, given in Java glob syntax"
-                            },
-                            "enum": {
-                                "type": "array",
-                                "description": "List of allowed values for the output channel",
-                                "items": {
-                                    "type": ["string", "number", "boolean", "array", "object"]
-                                },
-                                "uniqueItems": true
-                            }
-                        },
-                        "required": ["type", "description"]
-                    }
-                }
+                "type": "object", "items": { "$ref": "#/definitions/elementProperties" }
             }
         },
         "tools": {
@@ -160,6 +98,11 @@
                                 "minItems": 1,
                                 "uniqueItems": true,
                                 "message": "Licence must be an array of one or more entries, e.g. [\"MIT\"]"
+                            },
+                            "identifier": {
+                                "type": "string",
+                                "description": "bio.tools identifier of the tool",
+                                "pattern": "^biotools:.*$"
                             }
                         },
                         "required": ["description"],
@@ -182,5 +125,53 @@
             }
         }
     },
+    "definitions": {
+        "elementProperties": {
+            "type": "object",
+            "patternProperties": {
+                ".*": {
+                    "type": "object",
+                    "properties": {
+                        "type": {
+                            "type": "string",
+                            "description": "Type of the channel element",
+                            "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"]
+                        },
+                        "description": {
+                            "type": "string",
+                            "description": "Description of the channel"
+                        },
+                        "pattern": {
+                            "type": "string",
+                            "description": "Pattern of the channel, given in Java glob syntax"
+                        },
+                        "enum": {
+                            "type": "array",
+                            "description": "List of allowed values for the channel",
+                            "items": {
+                                "type": ["string", "number", "boolean", "array", "object"]
+                            },
+                            "uniqueItems": true
+                        },
+                        "ontologies": {
+                            "type": "array",
+                            "description": "List of ontologies for the channel",
+                            "uniqueItems": true,
+                            "items": {
+                                "type": "object",
+                                "patternProperties": {
+                                    ".*": {
+                                        "type": "string",
+                                        "pattern": "^(http|https)://.*"
+                                    }
+                                }
+                            }
+                        }
+                    },
+                    "required": ["type", "description"]
+                }
+            }
+        }
+    },
     "required": ["name", "description", "keywords", "authors", "output", "tools"]
 }