diff --git a/nf_core/pipeline-template/nextflow_schema.json b/nf_core/pipeline-template/nextflow_schema.json
index 97359a1f93..e2aac58cc0 100644
--- a/nf_core/pipeline-template/nextflow_schema.json
+++ b/nf_core/pipeline-template/nextflow_schema.json
@@ -243,10 +243,10 @@
         {
             "$ref": "#/$defs/input_output_options"
         },
-        {% if igenomes %}{
+        {%- if igenomes %}{
             "$ref": "#/$defs/reference_genome_options"
         },{% endif %}
-        {% if nf_core_configs %}{
+        {%- if nf_core_configs %}{
             "$ref": "#/$defs/institutional_config_options"
         },{% endif %}
         {
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 1c1821793c..bcc0fbd6b5 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -267,10 +267,15 @@ def init_pipeline(self):
         if not self.no_git:
             self.git_init_pipeline()
             # Run prettier on files
-            current_dir = Path.cwd()
-            os.chdir(self.outdir)
-            run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")])
-            os.chdir(current_dir)
+            if (
+                self.config.skip_features is None
+                or "code_linters" not in self.config.skip_features
+                or "github" not in self.config.skip_features
+            ):
+                current_dir = Path.cwd()
+                os.chdir(self.outdir)
+                run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")])
+                os.chdir(current_dir)
 
         if self.config.is_nfcore and not self.is_interactive:
             log.info(