From d90751160941fa8c14519fcb3c647f26c1ce1a6c Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 8 May 2026 13:28:57 +0200
Subject: [PATCH 1/3] forward `--verbose` to prek

---
 nf_core/pipelines/lint_utils.py | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/nf_core/pipelines/lint_utils.py b/nf_core/pipelines/lint_utils.py
index e1980cf89d..a17477cd8e 100644
--- a/nf_core/pipelines/lint_utils.py
+++ b/nf_core/pipelines/lint_utils.py
@@ -4,6 +4,7 @@
 import sys
 from pathlib import Path
 
+import click
 import git
 import rich
 import yaml
@@ -149,6 +150,12 @@ def run_prettier_on_file(file: Path | str | list[str]) -> None:
     Warns:
         If Prettier is not installed, a warning is logged.
     """
+    verbose = False
+    try:
+        ctx = click.get_current_context()
+        verbose = bool(ctx.obj and ctx.obj.get("verbose", False))
+    except RuntimeError:
+        pass
 
     is_git = check_git_repo()
 
@@ -160,6 +167,8 @@ def run_prettier_on_file(file: Path | str | list[str]) -> None:
     prek_bin = Path(sys.executable).parent / "prek"
     prek = str(prek_bin) if prek_bin.exists() else "prek"
     args = [prek, "run", "--config", str(nf_core_pre_commit_config), "prettier"]
+    if verbose:
+        args.append("--verbose")
     if isinstance(file, list):
         args.extend(["--files", *file])
     else:

From 133076422aa34385490a6745cde84aff9aa992d0 Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 8 May 2026 13:30:16 +0200
Subject: [PATCH 2/3] avoid prek input overload, by applying git- and
 prettieringore rules before handing it to prek

---
 nf_core/pipelines/create/create.py | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index b1b9f45594..f99b5798bb 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -12,6 +12,7 @@
 import git
 import git.config
 import jinja2
+import pathspec
 import yaml
 
 import nf_core
@@ -26,6 +27,19 @@
 log = logging.getLogger(__name__)
 
 
+def _get_prettier_files(outdir: Path) -> list[str]:
+    """Return non-gitignored files in outdir, further filtered by .prettierignore if present."""
+    repo = git.Repo(outdir)
+    files = [f for f in repo.git.ls_files("--cached", "--others", "--exclude-standard").splitlines() if f]
+
+    prettierignore = outdir / ".prettierignore"
+    if prettierignore.exists() and files:
+        spec = pathspec.PathSpec.from_lines("gitwildmatch", prettierignore.read_text().splitlines())
+        files = [f for f in files if not spec.match_file(f)]
+
+    return [str(outdir / f) for f in files]
+
+
 class PipelineCreate:
     """Creates a nf-core pipeline a la carte from the nf-core best-practice template.
 
@@ -281,7 +295,7 @@ def init_pipeline(self):
             ):
                 current_dir = Path.cwd()
                 os.chdir(self.outdir)
-                run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")])
+                run_prettier_on_file(_get_prettier_files(self.outdir))
                 os.chdir(current_dir)
 
         if self.config.is_nfcore and not self.is_interactive:
@@ -399,7 +413,7 @@ def render_template(self) -> None:
 
         # Run prettier on files for pipelines sync
         log.debug("Running prettier on pipeline files")
-        run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")])
+        run_prettier_on_file(_get_prettier_files(self.outdir))
 
     def fix_linting(self):
         """

From cea43bbe3d4958c319a543b5b44e8e0cadea321a Mon Sep 17 00:00:00 2001
From: mashehu <mashehu3@gmail.com>
Date: Fri, 8 May 2026 14:20:54 +0200
Subject: [PATCH 3/3] add fall back for non-git repos

---
 nf_core/pipelines/create/create.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py
index f99b5798bb..3fd3ecb258 100644
--- a/nf_core/pipelines/create/create.py
+++ b/nf_core/pipelines/create/create.py
@@ -29,8 +29,11 @@
 
 def _get_prettier_files(outdir: Path) -> list[str]:
     """Return non-gitignored files in outdir, further filtered by .prettierignore if present."""
-    repo = git.Repo(outdir)
-    files = [f for f in repo.git.ls_files("--cached", "--others", "--exclude-standard").splitlines() if f]
+    try:
+        repo = git.Repo(outdir)
+        files = [f for f in repo.git.ls_files("--cached", "--others", "--exclude-standard").splitlines() if f]
+    except git.InvalidGitRepositoryError:
+        files = [str(f.relative_to(outdir)) for f in outdir.rglob("*") if f.is_file()]
 
     prettierignore = outdir / ".prettierignore"
     if prettierignore.exists() and files: