Actually, let's make non-use of iGenomes the default

Author: pinin4fjords

docs/usage.md

@@ -206,8 +206,6 @@ nextflow run \
     --outdir <OUTDIR> \
     --gtf <GTF> \
     --fasta <GENOME FASTA> \
-    --igenomes_ignore \
-    --genome null \
     -profile docker
 ```
 

nextflow.config

@@ -22,7 +22,7 @@ params {
     gencode                    = false
     save_reference             = false
     igenomes_base              = 's3://ngi-igenomes/igenomes'
-    igenomes_ignore            = false
+    load_igenomes              = false
 
     // UMI handling
     with_umi                   = false
@@ -266,7 +266,7 @@ plugins {
 }
 
 // Load igenomes.config if required
-if (!params.igenomes_ignore) {
+if (params.load_igenomes) {
     includeConfig 'conf/igenomes.config'
 } else {
     params.genomes = [:]

nextflow_schema.json

@@ -331,12 +331,12 @@
                     "fa_icon": "fas fa-cloud-download-alt",
                     "hidden": true
                 },
-                "igenomes_ignore": {
+                "load_igenomes": {
                     "type": "boolean",
-                    "description": "Do not load the iGenomes reference config.",
+                    "description": "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`."
+                    "help_text": "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`."
                 }
             },
             "required": ["fasta"]