Fix http json schema URLs

nf-core · Oct 16, 2024 · cc6bff6 · cc6bff6
1 parent a634d32
commit cc6bff6
Show file tree

Hide file tree

Showing 4 changed files with 53 additions and 19 deletions.
diff --git a/assets/schema_annotation.json b/assets/schema_annotation.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/circrna/master/assets/schema_annotation.json",
     "title": "nf-core/circrna pipeline - params.annotation schema",
     "description": "Schema for the file provided with params.annotation",
@@ -11,7 +11,9 @@
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Annotation file name must be provided and cannot contain spaces",
-                "meta": ["id"]
+                "meta": [
+                    "id"
+                ]
             },
             "file": {
                 "type": "string",
@@ -26,9 +28,14 @@
                 "maximum": 1,
                 "default": 0.9,
                 "errorMessage": "Minimum overlap must be a number between 0 and 1",
-                "meta": ["min_overlap"]
+                "meta": [
+                    "min_overlap"
+                ]
             }
         },
-        "required": ["name", "file"]
+        "required": [
+            "name",
+            "file"
+        ]
     }
-}
+}
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/circrna/master/assets/schema_input.json",
     "title": "nf-core/circrna pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
@@ -11,7 +11,9 @@
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
-                "meta": ["id"]
+                "meta": [
+                    "id"
+                ]
             },
             "fastq_1": {
                 "type": "string",
@@ -29,12 +31,22 @@
             },
             "strandedness": {
                 "type": "string",
-                "enum": ["unstranded", "forward", "reverse", "auto"],
+                "enum": [
+                    "unstranded",
+                    "forward",
+                    "reverse",
+                    "auto"
+                ],
                 "default": "auto",
                 "errorMessage": "Strandedness must be one of 'unstranded', 'forward', 'reverse' or 'auto'",
-                "meta": ["strandedness"]
+                "meta": [
+                    "strandedness"
+                ]
             }
         },
-        "required": ["sample", "fastq_1"]
+        "required": [
+            "sample",
+            "fastq_1"
+        ]
     }
-}
+}
diff --git a/assets/schema_phenotype.json b/assets/schema_phenotype.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/circrna/master/assets/schema_phenotype.json",
     "title": "nf-core/circrna pipeline - params.phenotype schema",
     "description": "Schema for the file provided with params.phenotype",
@@ -18,6 +18,9 @@
                 "errorMessage": "Condition name must be provided and cannot contain spaces"
             }
         },
-        "required": ["sample", "condition"]
+        "required": [
+            "sample",
+            "condition"
+        ]
     }
-}
+}
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "http://json-schema.org/draft-07/schema",
+    "$schema": "https://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/circrna/master/nextflow_schema.json",
     "title": "nf-core/circrna pipeline parameters",
     "description": "Quantification, miRNA target prediction and differential expression analysis of circular RNAs",
@@ -10,7 +10,10 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "outdir"],
+            "required": [
+                "input",
+                "outdir"
+            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -59,7 +62,9 @@
             "type": "object",
             "fa_icon": "fas fa-circle-notch",
             "description": "Parameters for circrna discovery.",
-            "required": ["tools"],
+            "required": [
+                "tools"
+            ],
             "properties": {
                 "tools": {
                     "type": "string",
@@ -521,7 +526,14 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "enum": [
+                        "symlink",
+                        "rellink",
+                        "link",
+                        "copy",
+                        "copyNoFollow",
+                        "move"
+                    ],
                     "hidden": true
                 },
                 "email": {
@@ -649,4 +661,4 @@
             "$ref": "#/definitions/generic_options"
         }
     ]
-}
+}