diff --git a/CHANGELOG.md b/CHANGELOG.md
index f0a726768a..62c5dd5765 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -269,6 +269,7 @@ Another big release with lots of new features and bug fixes. Thanks to all contr
 - Convert `console` snippets to `bash` snippets in the template where applicable ([#1729](https://github.com/nf-core/tools/pull/1729))
 - Add `branch` field to module entries in `modules.json` to record what branch a module was installed from ([#1728](https://github.com/nf-core/tools/issues/1728))
 - Add customisation option to remove all GitHub support with `nf-core create` ([#1766](https://github.com/nf-core/tools/pull/1766))
+- Incorrect config parameter warnings when customising pipeline template ([#2333](https://github.com/nf-core/tools/pull/2333))
 
 ### Linting
 
diff --git a/nf_core/pipeline-template/lib/WorkflowMain.groovy b/nf_core/pipeline-template/lib/WorkflowMain.groovy
index b6c3336f26..5824dae2fb 100755
--- a/nf_core/pipeline-template/lib/WorkflowMain.groovy
+++ b/nf_core/pipeline-template/lib/WorkflowMain.groovy
@@ -49,8 +49,8 @@ class WorkflowMain {
             Nextflow.error("Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'")
         }
     }
-    {% if igenomes -%}
 
+    {%- if igenomes %}
     //
     // Get attribute from genome config file e.g. fasta
     //
@@ -62,4 +62,5 @@ class WorkflowMain {
         }
         return null
     }
-{% endif -%}}
+    {%- endif %}
+}
diff --git a/nf_core/pipeline-template/main.nf b/nf_core/pipeline-template/main.nf
index 561f2f6384..73984cb8fc 100644
--- a/nf_core/pipeline-template/main.nf
+++ b/nf_core/pipeline-template/main.nf
@@ -7,7 +7,7 @@
 {%- if branded %}
     Website: https://nf-co.re/{{ short_name }}
     Slack  : https://nfcore.slack.com/channels/{{ short_name }}
-{% endif -%}
+{%- endif %}
 ----------------------------------------------------------------------------------------
 */
 
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index e329b3e6fe..a1ca2e6157 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -13,12 +13,14 @@ params {
     // Input options
     input                      = null
 
-{% if igenomes %}
+    {%- if igenomes %}
     // References
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes'
     igenomes_ignore            = false
-    {% endif -%}
+    {% else %}
+    fasta                      = null
+    {%- endif %}
 
     // MultiQC options
     multiqc_config             = null
@@ -37,17 +39,18 @@ params {
     hook_url                   = null
     help                       = false
     version                    = false
-{% if nf_core_configs %}
 
     // Config options
+    config_profile_name        = null
+    config_profile_description = null
+
+    {%- if nf_core_configs %}
     custom_config_version      = 'master'
     custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
-    config_profile_description = null
     config_profile_contact     = null
     config_profile_url         = null
-    config_profile_name        = null
+    {% endif %}
 
-{% endif %}
     // Max resource options
     // Defaults only, expecting to be overwritten
     max_memory                 = '128.GB'
@@ -81,7 +84,7 @@ try {
 // } catch (Exception e) {
 //   System.err.println("WARNING: Could not load nf-core/config/{{ short_name }} profiles: ${params.custom_config_base}/pipeline/{{ short_name }}.config")
 // }
-{% endif %}
+{% endif -%}
 
 profiles {
     debug {
@@ -188,14 +191,14 @@ plugins {
     id 'nf-validation@0.2.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
-{% if igenomes %}
+{% if igenomes -%}
 // Load igenomes.config if required
 if (!params.igenomes_ignore) {
     includeConfig 'conf/igenomes.config'
 } else {
     params.genomes = [:]
 }
-{% endif %}
+{% endif -%}
 
 // Export these variables to prevent local Python/R libraries from conflicting with those in the container
 // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.