run pre-commit from a git repo

nf_core/pipelines/create/create.py

@@ -266,6 +266,11 @@ def init_pipeline(self):
         # Init the git repository and make the first commit
         if not self.no_git:
             self.git_init_pipeline()
+            # Run prettier on files
+            current_dir = Path.cwd()
+            os.chdir(self.outdir)
+            run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")])
+            os.chdir(current_dir)
 
         if self.config.is_nfcore and not self.is_interactive:
             log.info(
@@ -378,9 +383,6 @@ def render_template(self) -> None:
                     yaml.safe_dump(config_yml.model_dump(exclude_none=True), fh)
                     log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'")
 
-        # Run prettier on files
-        run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")])
-
     def fix_linting(self):
         """
         Updates the .nf-core.yml with linting configurations

nf_core/pipelines/lint_utils.py

@@ -97,7 +97,7 @@ def run_prettier_on_file(file: Union[Path, str, List[str]]) -> None:
             all_lines = [line for line in e.stdout.decode().split("\n")]
             files = "\n".join(all_lines[3:])
             log.debug(f"The following files were modified by prettier:\n {files}")
-        elif e.stderr.decode():
+        else:
             log.warning(
                 "There was an error running the prettier pre-commit hook.\n"
                 f"STDOUT: {e.stdout.decode()}\nSTDERR: {e.stderr.decode()}"