From 10d951612dbb0598ded0b6c02dd6241f84f648d4 Mon Sep 17 00:00:00 2001
From: Nico Trummer <nictru32@gmail.com>
Date: Wed, 16 Oct 2024 11:59:43 +0200
Subject: [PATCH] Fix problematic json schemas

---
 assets/schema_input.json                      | 35 ++++++++++++++-----
 nextflow_schema.json                          | 18 +++++++---
 .../tests/nextflow_schema.json                | 17 ++++++---
 3 files changed, 53 insertions(+), 17 deletions(-)

diff --git a/assets/schema_input.json b/assets/schema_input.json
index b5ff417..775aa5f 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$schema": "https://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/tfactivity/master/assets/schema_input.json",
     "title": "nf-core/tfactivity pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
@@ -11,19 +11,25 @@
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Sample name must be provided and cannot contain spaces",
-                "meta": ["id"]
+                "meta": [
+                    "id"
+                ]
             },
             "condition": {
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Condition name must be provided and cannot contain spaces",
-                "meta": ["condition"]
+                "meta": [
+                    "condition"
+                ]
             },
             "assay": {
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Assay name must be provided and cannot contain spaces",
-                "meta": ["assay"]
+                "meta": [
+                    "assay"
+                ]
             },
             "peak_file": {
                 "type": "string",
@@ -36,22 +42,33 @@
                 "type": "boolean",
                 "default": true,
                 "errorMessage": "footprinting must be a boolean value",
-                "meta": ["footprinting"]
+                "meta": [
+                    "footprinting"
+                ]
             },
             "include_original": {
                 "type": "boolean",
                 "default": true,
                 "errorMessage": "include_original must be a boolean value",
-                "meta": ["include_original"]
+                "meta": [
+                    "include_original"
+                ]
             },
             "max_peak_gap": {
                 "type": "integer",
                 "default": 500,
                 "minimum": 0,
                 "errorMessage": "max_peak_gap must be a positive integer",
-                "meta": ["max_peak_gap"]
+                "meta": [
+                    "max_peak_gap"
+                ]
             }
         },
-        "required": ["sample", "condition", "assay", "peak_file"]
+        "required": [
+            "sample",
+            "condition",
+            "assay",
+            "peak_file"
+        ]
     }
-}
+}
\ No newline at end of file
diff --git a/nextflow_schema.json b/nextflow_schema.json
index a0ee139..4f22c44 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$schema": "https://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/nf-core/tfactivity/master/nextflow_schema.json",
     "title": "nf-core/tfactivity pipeline parameters",
     "description": "TBD",
@@ -10,7 +10,10 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "outdir"],
+            "required": [
+                "input",
+                "outdir"
+            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -378,7 +381,14 @@
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",
-                    "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
+                    "enum": [
+                        "symlink",
+                        "rellink",
+                        "link",
+                        "copy",
+                        "copyNoFollow",
+                        "move"
+                    ],
                     "hidden": true
                 },
                 "email_on_fail": {
@@ -468,4 +478,4 @@
             "$ref": "#/$defs/generic_options"
         }
     ]
-}
+}
\ No newline at end of file
diff --git a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
index 331e0d2..927b4e7 100644
--- a/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
+++ b/subworkflows/nf-core/utils_nfschema_plugin/tests/nextflow_schema.json
@@ -1,5 +1,5 @@
 {
-    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "$schema": "https://json-schema.org/draft-07/schema",
     "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
     "title": ". pipeline parameters",
     "description": "",
@@ -10,7 +10,9 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["outdir"],
+            "required": [
+                "outdir"
+            ],
             "properties": {
                 "validate_params": {
                     "type": "boolean",
@@ -74,7 +76,14 @@
                     "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
                 },
                 "monochrome_logs": {
@@ -93,4 +102,4 @@
             "$ref": "#/$defs/generic_options"
         }
     ]
-}
+}
\ No newline at end of file