Add patch for nfschema plugin

Author: DLBPointon

nextflow_schema.json

@@ -10,7 +10,12 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "sample", "outdir", "map_order"],
+            "required": [
+                "input",
+                "sample",
+                "outdir",
+                "map_order"
+            ],
             "properties": {
                 "input": {
                     "type": "string",
@@ -50,7 +55,12 @@
                     "description": "Type of longread data",
                     "help_text": "Choose between {'hifi', 'clr', 'ont', 'illumina'}",
                     "fa_icon": "fas fa-file-signature",
-                    "enum": ["hifi", "clr", "ont", "illumina"]
+                    "enum": [
+                        "hifi",
+                        "clr",
+                        "ont",
+                        "illumina"
+                    ]
                 },
                 "cram": {
                     "type": "array",
@@ -75,14 +85,21 @@
                     "description": "HiC map scaffold order. Default to unsorted",
                     "help_text": "How you want to display your hic map, sorted by length?",
                     "fa_icon": "fas fa-file-signature",
-                    "enum": ["length", "unsorted"]
+                    "enum": [
+                        "length",
+                        "unsorted"
+                    ]
                 },
                 "aligner": {
                     "type": "string",
                     "description": "Aligner for use {minimap2, bwamem2} in generating map",
                     "help_text": "Pick between {minimap2, bwamem2, AUTO}. Defaults to 'minimap2'",
                     "fa_icon": "fas fa-file-signature",
-                    "enum": ["bwamem2", "minimap2", "AUTO"]
+                    "enum": [
+                        "bwamem2",
+                        "minimap2",
+                        "AUTO"
+                    ]
                 },
                 "run_hires": {
                     "type": "boolean",
@@ -95,7 +112,11 @@
                     "description": "Run Ultra resolution pretext maps",
                     "help_text": "Switch for Ultra resolution pretextmap generation",
                     "fa_icon": "fas fa-check",
-                    "enum": ["yes", "no", "force"]
+                    "enum": [
+                        "yes",
+                        "no",
+                        "force"
+                    ]
                 },
                 "cram_chunk_size": {
                     "type": "integer",
@@ -113,6 +134,13 @@
                     "exists": true,
                     "pattern": ".*\\.bam$"
                 },
+                "snapshot_order": {
+                    "type": "string",
+                    "format": "file-path",
+                    "description": "Order of scaffolds in the png",
+                    "help_text": "Order of scaffolds in the pretext snapshotpng",
+                    "fa_icon": "fas fa-sort"
+                },
                 "outdir": {
                     "type": "string",
                     "format": "directory-path",
@@ -216,7 +244,14 @@
                     "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": {
@@ -273,7 +308,10 @@
                     "hidden": true
                 },
                 "help": {
-                    "type": ["boolean", "string"],
+                    "type": [
+                        "boolean",
+                        "string"
+                    ],
                     "description": "Display the help message."
                 },
                 "help_full": {