enable setting defaulBranch for pipeline repo creation

CHANGELOG.md

@@ -18,6 +18,7 @@
 - Update subworkflows install so it installs also imported modules and subworkflows ([#1904](https://github.com/nf-core/tools/pull/1904))
 - Improve test coverage of sync.py
 - `check_up_to_date()` function from `modules_json` also checks for subworkflows.
+- The default branch can now be specified when creating a new pipeline repo [#1959](https://github.com/nf-core/tools/pull/1959).
 
 ### Modules
 

nf_core/create.py

@@ -40,6 +40,8 @@ class PipelineCreate(object):
  May the force be with you.
  outdir (str): Path to the local output directory.
  template_yaml (str): Path to template.yml file for pipeline creation settings.
+ plain (bool): If true the Git repository will be initialized plain.
+ default_branch (str): Specifies the --initial-branch name.
  """
 
  def __init__(
@@ -53,6 +55,7 @@ def __init__(
  outdir=None,
  template_yaml_path=None,
  plain=False,
+ default_branch=None,
  ):
  self.template_params, skip_paths_keys = self.create_param_dict(
  name, description, author, version, template_yaml_path, plain
@@ -82,6 +85,7 @@ def __init__(
  self.no_git = (
  no_git if self.template_params["github"] else True
  ) # Set to True if template was configured without github hosting
+ self.default_branch = default_branch
  self.force = force
  if outdir is None:
  outdir = os.path.join(os.getcwd(), self.template_params["name_noslash"])
@@ -523,24 +527,27 @@ def git_init_pipeline(self):
  Raises:
  UserWarning: if Git default branch is set to 'dev' or 'TEMPLATE'.
  """
- # Check that the default branch is not dev
+ default_branch = self.default_branch
  try:
- default_branch = git.config.GitConfigParser().get_value("init", "defaultBranch")
+ default_branch = default_branch or git.config.GitConfigParser().get_value("init", "defaultBranch")
  except configparser.Error:
- default_branch = None
  log.debug("Could not read init.defaultBranch")
- if default_branch == "dev" or default_branch == "TEMPLATE":
+ if default_branch in ["dev", "TEMPLATE"]:
  raise UserWarning(
- f"Your Git defaultBranch is set to '{default_branch}', which is incompatible with nf-core.\n"
- "This can be modified with the command [white on grey23] git config --global init.defaultBranch <NAME> [/]\n"
- "Pipeline git repository is not initialised."
+ f"Your Git defaultBranch '{default_branch}' is incompatible with nf-core.\n"
+ "'dev' and 'TEMPLATE' can not be used as default branch name.\n"
+ "Set the default branch name with "
+ "[white on grey23] git config --global init.defaultBranch <NAME> [/]\n"
+ "Or set the default_branch parameter in this class.\n"
+ "Pipeline git repository will not be initialised."
  )
- # Initialise pipeline
+
  log.info("Initialising pipeline git repository")
  repo = git.Repo.init(self.outdir)
+ if default_branch:
+ repo.active_branch.rename(default_branch)
  repo.git.add(A=True)
  repo.index.commit(f"initial template build from nf-core/tools, version {nf_core.__version__}")
- # Add TEMPLATE branch to git repository
  repo.git.branch("TEMPLATE")
  repo.git.branch("dev")
  log.info(

tests/test_create.py

@@ -4,6 +4,8 @@
 import os
 import unittest
 
+import git
+
 import nf_core.create
 
 from .utils import with_temporary_folder
@@ -16,6 +18,7 @@ def setUp(self, tmp_path):
  self.pipeline_description = "just for 4w3s0m3 tests"
  self.pipeline_author = "Chuck Norris"
  self.pipeline_version = "1.0.0"
+ self.default_branch = "default"
 
  self.pipeline = nf_core.create.PipelineCreate(
  name=self.pipeline_name,
@@ -26,6 +29,7 @@ def setUp(self, tmp_path):
  force=True,
  outdir=tmp_path,
  plain=True,
+ default_branch=self.default_branch,
  )
 
  def test_pipeline_creation(self):
@@ -37,3 +41,4 @@ def test_pipeline_creation(self):
  def test_pipeline_creation_initiation(self):
  self.pipeline.init_pipeline()
  assert os.path.isdir(os.path.join(self.pipeline.outdir, ".git"))
+ assert f" {self.default_branch}\n" in git.Repo.init(self.pipeline.outdir).git.branch()

tests/test_sync.py

@@ -26,12 +26,14 @@ def setUp(self):
  """Create a new pipeline to test"""
  self.tmp_dir = tempfile.mkdtemp()
  self.pipeline_dir = os.path.join(self.tmp_dir, "test_pipeline")
+ default_branch = "master"
  self.create_obj = nf_core.create.PipelineCreate(
- "testing", "test pipeline", "tester", outdir=self.pipeline_dir, plain=True
+ "testing", "test pipeline", "tester", outdir=self.pipeline_dir, plain=True, default_branch=default_branch
  )
  self.create_obj.init_pipeline()
  self.remote_path = os.path.join(self.tmp_dir, "remote_repo")
  self.remote_repo = git.Repo.init(self.remote_path, bare=True)
+ self.remote_repo.active_branch.rename(default_branch)
 
  def tearDown(self):
  if os.path.exists(self.tmp_dir):