From e9cde5910a6ebd3e8bccef91a84ee9a47a56381a Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 12:17:54 +0100
Subject: [PATCH 1/2] set default_branch to master for now

---
 nf_core/pipeline-template/nextflow.config | 2 +-
 nf_core/pipelines/create/create.py        | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
index 000d7cd66..36018b106 100644
--- a/nf_core/pipeline-template/nextflow.config
+++ b/nf_core/pipeline-template/nextflow.config
@@ -327,7 +327,7 @@ validation {
     https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-    https://github.com/{{ name }}/blob/master/CITATIONS.md
+    https://github.com/{{ name }}/blob/{{ default_branch }}/CITATIONS.md
 """{% endif %}
     }{% if is_nfcore %}
     summary {
diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index 8855f2dae..ae5bea57d 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -57,7 +57,7 @@ def __init__(
         template_config: Optional[Union[CreateConfig, str, Path]] = None,
         organisation: str = "nf-core",
         from_config_file: bool = False,
-        default_branch: str = "main",
+        default_branch: str = "master",
         is_interactive: bool = False,
     ) -> None:
         if isinstance(template_config, CreateConfig):
@@ -431,8 +431,8 @@ def get_default_branch(self) -> None:
         """Gets the default branch name from the Git configuration."""
         try:
             self.default_branch = (
-                str(git.config.GitConfigParser().get_value("init", "defaultBranch")) or "main"
-            )  # default to main
+                str(git.config.GitConfigParser().get_value("init", "defaultBranch")) or "master"
+            )  # default to master
         except configparser.Error:
             log.debug("Could not read init.defaultBranch")
         if self.default_branch in ["dev", "TEMPLATE"]:

From 7110fff5287cdeb2e5e769d7cf18bd725436f0ad Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Tue, 10 Dec 2024 12:20:01 +0100
Subject: [PATCH 2/2] update changelog

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

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9015ac6da..4eef49da4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -81,6 +81,7 @@
 - Parallelize pipeline GHA tests over docker/conda/singularity ([#3214](https://github.com/nf-core/tools/pull/3214))
 - Fix `template_version_comment.yml` github action ([#3212](https://github.com/nf-core/tools/pull/3212))
 - Fix pre-commit linting on pipeline template ([#3218](https://github.com/nf-core/tools/pull/3218))
+- set default_branch to master for now ([#3335](https://github.com/nf-core/tools/issues/3335))
 
 ### Linting