diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 2be5f632ec..b6d7337714 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -67,13 +67,6 @@ try {
     System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
 }
 
-// Load igenomes.config if required
-if (!params.igenomes_ignore) {
-    includeConfig 'conf/igenomes.config'
-} else {
-    params.genomes = [:]
-}
-
 profiles {
     debug { process.beforeScript = 'echo $HOSTNAME' }
     conda {
@@ -125,6 +118,13 @@ profiles {
     test_full { includeConfig 'conf/test_full.config' }
 }
 
+// Load igenomes.config if required
+if (!params.igenomes_ignore) {
+    includeConfig 'conf/igenomes.config'
+} else {
+    params.genomes = [:]
+}
+
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 env {
     PYTHONNOUSERSITE = 1