Git default branch

CHANGELOG.md

@@ -10,6 +10,7 @@
 - Add `CITATION.cff` [#361](https://github.com/nf-core/tools/issues/361)
 - Add Gitpod and Mamba profiles to the pipeline template ([#1673](https://github.com/nf-core/tools/pull/1673))
 - Remove call to `getGenomeAttribute` in `main.nf` when running `nf-core create` without iGenomes ([#1670](https://github.com/nf-core/tools/issues/1670))
+- Make `nf-core create` fail if Git default branch name is dev or TEMPLATE ([#1705](https://github.com/nf-core/tools/pull/1705))
 
 ### Linting
 

nf_core/create.py

@@ -2,6 +2,7 @@
 """Creates a nf-core pipeline matching the current
 organization's specification based on a template.
 """
+import configparser
 import imghdr
 import logging
 import os
@@ -490,7 +491,24 @@ def download_pipeline_logo(self, url, img_fn):
             break
 
     def git_init_pipeline(self):
-        """Initialises the new pipeline as a Git repository and submits first commit."""
+        """Initialises the new pipeline as a Git repository and submits first commit.
+
+        Raises:
+            UserWarning: if Git default branch is set to 'dev' or 'TEMPLATE'.
+        """
+        # Check that the default branch is not dev
+        try:
+            default_branch = 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":
+            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."
+            )
+        # Initialise pipeline
         log.info("Initialising pipeline git repository")
         repo = git.Repo.init(self.outdir)
         repo.git.add(A=True)