avoid prek input overload and forward --verbose to it

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 +27,22 @@
 log = logging.getLogger(__name__)
 
 
+def _get_prettier_files(outdir: Path) -> list[str]:
+    """Return non-gitignored files in outdir, further filtered by .prettierignore if present."""
+    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:
+        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 +298,7 @@ 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 +416,7 @@ 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):
         """

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: