From c9cf6980af9b84f68f613eee71732da8db0f950a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ren=C3=A9=20Rahn?= <1529364+rrahn@users.noreply.github.com>
Date: Fri, 16 Jan 2026 14:53:23 +0100
Subject: [PATCH 1/2] Escape original merge branch to compile regex

---
 nf_core/pipelines/sync.py    |  2 +-
 tests/pipelines/test_sync.py | 21 +++++++++++++++++++++
 2 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/nf_core/pipelines/sync.py b/nf_core/pipelines/sync.py
index 7ce358cd07..ee4dd1a8bf 100644
--- a/nf_core/pipelines/sync.py
+++ b/nf_core/pipelines/sync.py
@@ -371,7 +371,7 @@ def create_merge_base_branch(self):
         # Check if branch exists already
         branch_list = [b.name for b in self.repo.branches]
         if self.merge_branch in branch_list:
-            merge_branch_format = re.compile(rf"{self.original_merge_branch}-(\d+)")
+            merge_branch_format = re.compile(rf"{re.escape(self.original_merge_branch)}-(\d+)")
             max_branch = max(
                 [1]
                 + [
diff --git a/tests/pipelines/test_sync.py b/tests/pipelines/test_sync.py
index 746b2db76a..b32f21d3ee 100644
--- a/tests/pipelines/test_sync.py
+++ b/tests/pipelines/test_sync.py
@@ -396,6 +396,27 @@ def test_create_merge_base_branch_thrice(self):
         for branch_no in [2, 3]:
             assert f"{psync.original_merge_branch}-{branch_no}" in psync.repo.branches
 
+    def test_create_merge_base_branch_with_special_characters(self):
+        """Test that branch names with regex special characters (like +) are handled correctly.
+
+        This tests that the fix using re.escape() works properly when the version
+        contains characters that have special meaning in regex patterns (e.g., '+' in '3.6.0.dev0+local0').
+        Without re.escape(), the '+' would be interpreted as a regex quantifier instead of a literal character.
+        """
+        psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir)
+        psync.inspect_sync_dir()
+        psync.get_wf_config()
+
+        psync.original_merge_branch = "nf-core-template-merge-3.6.0.dev0+local0"
+        psync.merge_branch = psync.original_merge_branch
+
+        for _ in range(3):
+            psync.create_merge_base_branch()
+
+        assert psync.merge_branch in psync.repo.branches
+        for branch_no in [2, 3]:
+            assert f"{psync.original_merge_branch}-{branch_no}" in psync.repo.branches
+
     def test_push_merge_branch(self):
         """Try pushing merge branch"""
         psync = nf_core.pipelines.sync.PipelineSync(self.pipeline_dir)

From 6d30c03780985722a503a09bec7977213915f745 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Fri, 16 Jan 2026 14:02:15 +0000
Subject: [PATCH 2/2] [automated] Update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 724311e744..c28ba88d9b 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -18,6 +18,7 @@
 - Update astral-sh/setup-uv digest to ed21f2f ([#3959](https://github.com/nf-core/tools/pull/3959))
 - Update codecov/codecov-action digest to 671740a ([#3962](https://github.com/nf-core/tools/pull/3962))
 - Add support for SVG files in bump-version command ([#3978](https://github.com/nf-core/tools/pull/3978))
+- Escape original merge branch to compile regex ([#3984](https://github.com/nf-core/tools/pull/3984))
 
 ### Template