From b69906fa7a2df1cc2cd90d011814da96633d84f1 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Mon, 18 Mar 2024 10:30:18 +0000
Subject: [PATCH] Update schema

---
 nextflow_schema.json | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 6752d16..8bc2809 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -471,6 +471,14 @@
                 "extra_ribotish_predict_args": {
                     "type": "string",
                     "description": "Extra arguments to pass to the ribotish predict command in addition to defaults defined by the pipeline."
+                },
+                "extra_ribotricer_prepareorfs_args": {
+                    "type": "string",
+                    "description": "Extra arguments to pass to the ribotricer prepare-orfs command in addition to defaults defined by the pipeline."
+                },
+                "extra_ribotricer_detectorfs_args": {
+                    "type": "string",
+                    "description": "Extra arguments to pass to the ribotricer detect-orfs command in addition to defaults defined by the pipeline."
                 }
             }
         },
@@ -657,6 +665,9 @@
                     "type": "boolean",
                     "description": "Skip Ribo-TISH.",
                     "fa_icon": "fas fa-fast-forward"
+                },
+                "skip_ribotricer": {
+                    "type": "boolean"
                 }
             }
         },
@@ -870,9 +881,6 @@
         }
     },
     "allOf": [
-        {
-            "$ref": "#/definitions/riboseq_specific_options"
-        },
         {
             "$ref": "#/definitions/input_output_options"
         },
@@ -891,6 +899,9 @@
         {
             "$ref": "#/definitions/alignment_options"
         },
+        {
+            "$ref": "#/definitions/riboseq_specific_options"
+        },
         {
             "$ref": "#/definitions/optional_outputs"
         },