Fix schemas

Author: JoseEspinosa

assets/schema_input.json

@@ -42,20 +42,17 @@
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Antibody entry cannot contain spaces",
-                "dependentRequired": ["control"],
                 "meta": ["antibody"]
             },
             "control": {
                 "type": "string",
                 "pattern": "^\\S+$",
                 "errorMessage": "Control entry cannot contain spaces",
-                "dependentRequired": ["antibody", "control_replicate"],
                 "meta": ["control"]
             },
             "control_replicate": {
-                "type": "string",
-                "pattern": "^\\S+$",
-                "errorMessage": "Control entry cannot contain spaces",
+                "type": "integer",
+                "errorMessage": "Replicate id not an integer!",
                 "meta": ["control_replicate"]
             }
         },

conf/test.config

@@ -10,6 +10,7 @@
 ----------------------------------------------------------------------------------------
 */
 
+// Limit resources so that this can run on GitHub Actions
 process {
     resourceLimits = [
         cpus: 4,

nextflow_schema.json

@@ -163,25 +163,17 @@
                 "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
+                    "description": "The base path to the igenomes reference files",
+                    "fa_icon": "fas fa-ban",
+                    "hidden": true,
+                    "default": "s3://ngi-igenomes/igenomes/"
                 },
                 "igenomes_ignore": {
                     "type": "boolean",
                     "description": "Do not load the iGenomes reference config.",
                     "fa_icon": "fas fa-ban",
                     "hidden": true,
                     "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`."
-                },
-                "igenomes_base": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "description": "The base path to the igenomes reference files",
-                    "fa_icon": "fas fa-ban",
-                    "hidden": true,
-                    "default": "s3://ngi-igenomes/igenomes/"
                 }
             },
             "required": ["fasta"]