Add Nextflow schema

nextflow_schema.json

@@ -0,0 +1,70 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/Sage-Bionetworks-Workflows/nf-artist/dsl2/nextflow_schema.json",
+    "title": "Sage-Bionetworks-Workflows/nf-artist parameters",
+    "description": "Nextflow pipeline for generating Minerva stories and Miniature thumbnails from multiplexed tissue imaging datasets",
+    "type": "object",
+    "definitions": {
+        "input_output_options": {
+            "title": "Input/output options",
+            "type": "object",
+            "fa_icon": "fas fa-terminal",
+            "description": "Define where the pipeline should find input data and save output data.",
+           "required": ["input", "outdir"],
+            "properties": {
+                "input": {
+                    "type": "string",
+                    "format": "file-path",
+                    "mimetype": "text/csv",
+                    "description": "Path to a CSV samplesheet"
+                },
+                "outdir": {
+                    "type": "string",
+                    "description": "Directory in which outputs are placed",
+                    "default": "outputs"
+                }
+            }
+        },
+        "miniatue_options": {
+            "title": "Miniature options",
+            "type": "object",
+            "fa_icon": "fas fa-palette",
+            "description": "Define HTAN Artist pipeline parameters.",
+            "properties": {
+                "remove_bg": {
+                    "type": "boolean",
+                    "description": "Remove non-tissue background",
+                    "default": true
+                },
+                "level": {
+                    "type": "integer",
+                    "description": "The pyramid level used in thumbnauls, Default: -1 (smallest)",
+                    "default": -1
+                },
+                "dimred": {
+                    "type": "string",
+                    "description": "The dimensionality reduction method used",
+                    "default": "umap",
+                    "enum": ["umap", "tsne", "pca"]
+                },
+                "colormap": {
+                    "type": "string",
+                    "description": "The colormap used. Ensure colormap is compatiable with `n_components` selected ",
+                    "enum": ["UCIE", "LAB", "RGB", "BREMM", "SCHUMANN", "STEIGER", "TEULING2", "ZIEGLER","CUBEDIAGONAL"],
+                    "default": "UCIE"
+                },
+                "n_components": {
+                    "type": "integer",
+                    "description": "",
+                    "default": 3,
+                    "enum": [2,3]
+                }
+            }
+        }
+    },
+    "allOf": [
+        {
+            "$ref": "#/definitions/parameters"
+        }
+    ]
+}