diff --git a/CHANGELOG.md b/CHANGELOG.md
index c5ab9a512..0afc77cf5 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,7 @@
 
 - Keep pipeline name in version.yml file ([#3223](https://github.com/nf-core/tools/pull/3223))
 - Fix Manifest DOI text ([#3224](https://github.com/nf-core/tools/pull/3224))
+- Do not assume pipeline name is url ([#3225](https://github.com/nf-core/tools/pull/3225))
 
 ### Download
 
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 90e620069..0afaaa678 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -272,7 +272,7 @@ validation {
     defaultIgnoreParams = ["genomes"]
     help {
         enabled = true
-        command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
+        command = "nextflow run {{ name }} -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
         {% if is_nfcore -%}
@@ -283,7 +283,7 @@ validation {
 \033[0;34m  |\\ | |__  __ /  ` /  \\ |__) |__         \033[0;33m}  {\033[0m
 \033[0;34m  | \\| |       \\__, \\__/ |  \\ |___     \033[0;32m\\`-._,-`-,\033[0m
                                         \033[0;32m`._,._,\'\033[0m
-\033[0;35m  ${manifest.name} ${manifest.version}\033[0m
+\033[0;35m  {{ name }} ${manifest.version}\033[0m
 -\033[2m----------------------------------------------------\033[0m-
 """
         afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { "    https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""}
@@ -291,7 +291,7 @@ validation {
     https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-    https://github.com/${manifest.name}/blob/master/CITATIONS.md
+    https://github.com/{{ name }}/blob/master/CITATIONS.md
 """{% endif %}
     }{% if is_nfcore %}
     summary {