diff --git a/.github/workflows/sync.yml b/.github/workflows/sync.yml
index 15802cdef2..23b05de88a 100644
--- a/.github/workflows/sync.yml
+++ b/.github/workflows/sync.yml
@@ -15,6 +15,10 @@ on:
           - "ubuntu-latest"
           - "self-hosted"
         default: "self-hosted"
+      force_pr:
+        description: "Force a PR to be created"
+        type: boolean
+        default: false
 
 # Cancel if a newer run is started
 concurrency:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 4d4710976d..9a41f95e37 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -41,6 +41,7 @@
 
 - Update CI to use nf-core/setup-nextflow v2 ([#2819](https://github.com/nf-core/tools/pull/2819))
 - Changelog bot: handle also patch version before dev suffix ([#2820](https://github.com/nf-core/tools/pull/2820))
+- Add `force_pr` flag to sync, to force a PR even though there are no changes committed ([#2822](https://github.com/nf-core/tools/pull/2822))
 - Update prettier to 3.2.5 ([#2830](https://github.com/nf-core/tools/pull/2830))
 - Update GitHub Actions ([#2827](https://github.com/nf-core/tools/pull/2827)), ([#2902](https://github.com/nf-core/tools/pull/2902)), ([#2927](https://github.com/nf-core/tools/pull/2927)), ([#2939](https://github.com/nf-core/tools/pull/2939))
 - Switch to setup-nf-test ([#2834](https://github.com/nf-core/tools/pull/2834))
diff --git a/nf_core/__main__.py b/nf_core/__main__.py
index 39a1afbf63..147b0586b2 100644
--- a/nf_core/__main__.py
+++ b/nf_core/__main__.py
@@ -2147,10 +2147,16 @@ def logo(logo_text, dir, name, theme, width, format, force):
     default=False,
     help="Make a GitHub pull-request with the changes.",
 )
+@click.option(
+    "--force_pr",
+    is_flag=True,
+    default=False,
+    help="Force the creation of a pull-request, even if there are no changes.",
+)
 @click.option("-g", "--github-repository", type=str, help="GitHub PR: target repository.")
 @click.option("-u", "--username", type=str, help="GitHub PR: auth username.")
 @click.option("-t", "--template-yaml", help="Pass a YAML file to customize the template")
-def sync(dir, from_branch, pull_request, github_repository, username, template_yaml):
+def sync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr):
     """
     Sync a pipeline [cyan i]TEMPLATE[/] branch with the nf-core template.
 
@@ -2170,7 +2176,7 @@ def sync(dir, from_branch, pull_request, github_repository, username, template_y
     is_pipeline_directory(dir)
 
     # Sync the given pipeline dir
-    sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml)
+    sync_obj = PipelineSync(dir, from_branch, pull_request, github_repository, username, template_yaml, force_pr)
     try:
         sync_obj.sync()
     except (SyncExceptionError, PullRequestExceptionError) as e:
diff --git a/nf_core/sync.py b/nf_core/sync.py
index 93a79c3d50..5e7b198d8d 100644
--- a/nf_core/sync.py
+++ b/nf_core/sync.py
@@ -44,6 +44,7 @@ class PipelineSync:
         gh_username (str): GitHub username
         gh_repo (str): GitHub repository name
         template_yaml_path (str): Path to template.yml file for pipeline creation settings. DEPRECATED
+        force_pr (bool): Force the creation of a pull request, even if there are no changes to the template
 
     Attributes:
         pipeline_dir (str): Path to target pipeline directory
@@ -64,6 +65,7 @@ def __init__(
         gh_repo=None,
         gh_username=None,
         template_yaml_path=None,
+        force_pr=False,
     ):
         """Initialise syncing object"""
 
@@ -76,6 +78,7 @@ def __init__(
         self.make_pr = make_pr
         self.gh_pr_returned_data = {}
         self.required_config_vars = ["manifest.name", "manifest.description", "manifest.version", "manifest.author"]
+        self.force_pr = force_pr
 
         self.gh_username = gh_username
         self.gh_repo = gh_repo
@@ -132,8 +135,12 @@ def sync(self):
         self.make_template_pipeline()
         self.commit_template_changes()
 
+        if not self.made_changes and self.force_pr:
+            log.info("No changes made to TEMPLATE, but PR forced")
+            self.made_changes = True
+
         # Push and make a pull request if we've been asked to
-        if self.made_changes and self.make_pr:
+        if self.made_changes and self.make_pr or self.force_pr:
             try:
                 # Check that we have an API auth token
                 if os.environ.get("GITHUB_AUTH_TOKEN", "") == "":