updated default databases to null

nextflow.config

@@ -69,10 +69,10 @@ params {
 
 
     // Datasets
-    dehosting_idx = "./databases/PhiPacHum_m2.idx" // mm2 index
-    mash_sketch = "./databases/GTDBSketch_20231003.msh" // Make sure comments are formatted as taxonomic strings
-    bakta_db = "./databases/db-light"
-    kraken2_db = "./databases/k2_standard_20220607/"
+    dehosting_idx = null // mm2 index
+    mash_sketch = null // Make sure comments are formatted as taxonomic strings
+    bakta_db = null
+    kraken2_db = null
     staramr_db = null // Recommended usage is to use the default database in the container
 
 

nextflow_schema.json

@@ -76,28 +76,24 @@
             "properties": {
                 "dehosting_idx": {
                     "type": "string",
-                    "default": "./databases/PhiPacHum_m2.idx",
                     "description": "Mash sketch used for contamination detection and speciation (Sketch comments must be a taxonomic string similar to what Kraken2 outputs)",
                     "pattern": "^\\S+$",
                     "format": "file-path"
                 },
                 "mash_sketch": {
                     "type": "string",
-                    "default": "./databases/GTDBSketch_20231003.msh",
                     "description": "Minimpa2 index for dehosting and kitome removal",
                     "pattern": "^\\S+$",
                     "format": "file-path"
                 },
                 "bakta_db": {
                     "type": "string",
                     "description": "Database use for bakta, this value is optional as bakta can be skipped",
-                    "default": "./databases/db-light",
                     "pattern": "^\\S+$",
                     "format": "directory-path"
                 },
                 "kraken2_db": {
                     "type": "string",
-                    "default": "./databases/k2_standard_20220607/",
                     "description": "Kraken2 database",
                     "pattern": "^\\S+$",
                     "format": "directory-path"