From c9025ef26b3c059146e9a69841ac4b7d6cff4db2 Mon Sep 17 00:00:00 2001
From: Adam Taylor <adam.taylor@sagebase.org>
Date: Thu, 3 Aug 2023 21:06:42 +0100
Subject: [PATCH] Add Nextflow schema

---
 nextflow_schema.json | 56 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)
 create mode 100644 nextflow_schema.json

diff --git a/nextflow_schema.json b/nextflow_schema.json
new file mode 100644
index 0000000..3984ac8
--- /dev/null
+++ b/nextflow_schema.json
@@ -0,0 +1,56 @@
+{
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
+    "title": ". pipeline parameters",
+    "description": "",
+    "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",
+                    "exists": true,
+                    "mimetype": "text/csv",
+                    "pattern": "^\\S+\\.csv$",
+                    "description": "Path to comma-separated file containing information about the samples in the experiment.",
+                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.",
+                    "fa_icon": "fas fa-file-csv"
+                },
+                "outdir": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.",
+                    "fa_icon": "fas fa-folder-open"
+                }
+            }
+        }
+    },
+    "allOf": [
+        {
+            "$ref": "#/definitions/input_output_options"
+        }
+    ],
+    "properties": {
+        "outsuffix": {
+            "type": "string",
+            "default": "_cleaned"
+        },
+        "rm_svs_label": {
+            "type": "string",
+            "default": "true"
+        },
+        "rm_ome_sa": {
+            "type": "string",
+            "default": "true"
+        }
+    }
+}