From 00d29d1e276bc6bb9770ef5d717249da0b19fe5f Mon Sep 17 00:00:00 2001
From: mcmero <cmerom@gmail.com>
Date: Mon, 26 Feb 2024 15:31:01 +1100
Subject: [PATCH] Added shared conda env location

---
 nextflow.config      |  3 +++
 nextflow_schema.json | 28 +++++++++++++++++++++-------
 2 files changed, 24 insertions(+), 7 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index b0a1e1f..141539e 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -30,6 +30,9 @@ params {
     //if false, the database is queried to create one
     //if true, config.txt should be in the input directory
     is_config_file_provided = true
+
+    // if specified, use this location to load prebuilt conda environments
+    conda_env_location = ""
 }
 
 //SQL DB Plugin
diff --git a/nextflow_schema.json b/nextflow_schema.json
index f30ecfe..89d25e9 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -110,13 +110,24 @@
                     "default": false,
                     "description": "Optional ready-made config file for splitcode. Use this to skip the databse index lookup. Must be called config.txt and put in input directory."
                 }
-            },
-            "required": [
-                "fwd_primer",
-                "rev_primer",
-                "primer_mismatches",
-                "barcode_length"
-            ]
+            }
+        },
+        "generic_options": {
+            "title": "Generic options",
+            "type": "object",
+            "fa_icon": "fas fa-file-import",
+            "description": "Less common options for the pipeline, typically set in a config file.",
+            "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.",
+            "properties": {
+                "conda_env_location": {
+                    "type": "string",
+                    "format": "directory-path",
+                    "description": "Use this location for pre-build conda environments (if blank, new conda environments will be created).",
+                    "fa_icon": "fas fa-cog",
+                    "default": "",
+                    "hidden": true
+                }
+            }
         }
     },
     "allOf": [
@@ -128,6 +139,9 @@
         },
         {
             "$ref": "#/definitions/demultiplex_options"
+        },
+        {
+            "$ref": "#/definitions/generic_options"
         }
     ]
 }
\ No newline at end of file