From 2af46d8f29b8e3cea2324fe2336288af84c3fa15 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 16 Oct 2024 17:07:04 +0200
Subject: [PATCH] Comment out unusued tempalte parmaeter (renaming), and remove
 a duplicate entry in schema

---
 nextflow.config      | 2 +-
 nextflow_schema.json | 8 --------
 2 files changed, 1 insertion(+), 9 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index 11cc0e43..97554f03 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -150,7 +150,7 @@ params {
     save_mmseqs_db                       = false
 
     // References
-    genome                     = null
+    //genome                     = null // we use --host_genome instead
     igenomes_base              = 's3://ngi-igenomes/igenomes/'
     igenomes_ignore            = false
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3befcd0f..79312746 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -66,14 +66,6 @@
             "fa_icon": "fas fa-dna",
             "description": "Reference genome related files and options required for the workflow.",
             "properties": {
-                "igenomes_base": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "description": "Directory / URL base for iGenomes references.",
-                    "default": "s3://ngi-igenomes/igenomes/",
-                    "fa_icon": "fas fa-cloud-download-alt",
-                    "hidden": true
-                },
                 "igenomes_ignore": {
                     "type": "boolean",
                     "description": "Do not load the iGenomes reference config.",