format code blocks and admonitions

docs/migration_guide.md

@@ -30,8 +30,9 @@ sed -i -e 's/http:\/\/json-schema.org\/draft-07\/schema/https:\/\/json-schema.or
 This will replace the old schema draft specification (`draft-07`) by the new one (`2020-12`), and the old keyword `definitions` by the new notation `defs`.
 
 !!! note
-Repeat this command for every JSON schema you use in your pipeline. e.g. for the default samplesheet schema:
-`bash sed -i -e 's/http:\/\/json-schema.org\/draft-07\/schema/https:\/\/json-schema.org\/draft\/2020-12\/schema/g' -e 's/definitions/defs/g' assets/schema_input.json `
+
+    Repeat this command for every JSON schema you use in your pipeline. e.g. for the default samplesheet schema:
+    `bash sed -i -e 's/http:\/\/json-schema.org\/draft-07\/schema/https:\/\/json-schema.org\/draft\/2020-12\/schema/g' -e 's/definitions/defs/g' assets/schema_input.json `
 
 If you are using any special features in your schemas, you will need to update your schemas manually. Please refer to the [JSON Schema draft 2020-12 release notes](https://json-schema.org/draft/2020-12/release-notes) and [JSON schema draft 2019-09 release notes](https://json-schema.org/draft/2019-09/release-notes) for more information.
 
@@ -44,25 +45,121 @@ When you use `unique` in your schemas, you should update it to use `uniqueItems`
 If you used the `unique:true` field, you should update it to use `uniqueItems` like this:
 
 === "Before v2.0"
-`json hl_lines="9" { "$schema": "http://json-schema.org/draft-07/schema", "type": "array", "items": { "type": "object", "properties": { "sample": { "type": "string", "unique": true } } } } `
+
+    ```json hl_lines="9"
+    {
+        "$schema": "http://json-schema.org/draft-07/schema",
+        "type": "array",
+        "items": {
+            "type": "object",
+            "properties": {
+                "sample": {
+                    "type": "string",
+                    "unique": true
+                }
+            }
+        }
+    }
+    ```
 
 === "After v2.0"
-`json hl_lines="12" { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "array", "items": { "type": "object", "properties": { "sample": { "type": "string" } } }, "uniqueItems": true } `
+
+    ```json hl_lines="12"
+    {
+        "$schema": "https://json-schema.org/draft/2020-12/schema",
+        "type": "array",
+        "items": {
+            "type": "object",
+            "properties": {
+                "sample": {
+                    "type": "string"
+                }
+            }
+        },
+        "uniqueItems": true
+    }
+    ```
 
 If you used the `unique: ["field1", "field2"]` field, you should update it to use `uniqueEntries` like this:
 
 === "Before v2.0"
-`json hl_lines="9" { "$schema": "http://json-schema.org/draft-07/schema", "type": "array", "items": { "type": "object", "properties": { "sample": { "type": "string", "unique": ["sample"] } } } } `
+
+    ```json hl_lines="9"
+    {
+        "$schema": "http://json-schema.org/draft-07/schema",
+        "type": "array",
+        "items": {
+            "type": "object",
+            "properties": {
+                "sample": {
+                    "type": "string",
+                    "unique": ["sample"]
+                }
+            }
+        }
+    }
+    ```
 
 === "After v2.0"
-`json hl_lines="12" { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "array", "items": { "type": "object", "properties": { "sample": { "type": "string" } } }, "uniqueEntries": ["sample"] } `
+
+    ```json hl_lines="12"
+    {
+        "$schema": "https://json-schema.org/draft/2020-12/schema",
+        "type": "array",
+        "items": {
+            "type": "object",
+            "properties": {
+                "sample": {
+                    "type": "string"
+                }
+            }
+        },
+        "uniqueEntries": ["sample"]
+    }
+    ```
 
 ### Updating `dependentRequired` keyword
 
 When you use `dependentRequired` in your schemas, you should update it like this:
 
 === "Before v2.0"
-`json hl_lines="12" { "$schema": "http://json-schema.org/draft-07/schema", "type": "object", "properties": { "fastq_1": { "type": "string", "format": "file-path" }, "fastq_2": { "type": "string", "format": "file-path" "dependentRequired": ["fastq_1"] } } } `
+
+    ```json hl_lines="12"
+    {
+        "$schema": "http://json-schema.org/draft-07/schema",
+        "type": "object",
+        "properties": {
+            "fastq_1": {
+                "type": "string",
+                "format": "file-path"
+            },
+            "fastq_2": {
+                "type": "string",
+                "format": "file-path",
+                "dependentRequired": ["fastq_1"]
+            }
+        }
+    }
+    ```
 
 === "After v2.0"
-`json hl_lines="14 15 16" { "$schema": "https://json-schema.org/draft/2020-12/schema", "type": "object", "properties": { "fastq_1": { "type": "string", "format": "file-path" }, "fastq_2": { "type": "string", "format": "file-path" } }, "dependentRequired": { "fastq_2": ["fastq_1"] } } `
+
+    ```json hl_lines="14 15 16"
+    {
+        "$schema": "https://json-schema.org/draft/2020-12/schema",
+        "type": "object",
+        "properties": {
+            "fastq_1": {
+                "type": "string",
+                "format": "file-path"
+            },
+            "fastq_2": {
+                "type": "string",
+                "format": "file-path"
+            }
+        },
+        "dependentRequired": {
+            "fastq_2": ["fastq_1"]
+        }
+    }
+    ```