Add specific prettier-commit config for prettier check, improve log message

MANIFEST.in

@@ -4,4 +4,4 @@ graft nf_core/module-template
 graft nf_core/pipeline-template
 graft nf_core/subworkflow-template
 include requirements.txt
-include .pre-commit-config.yaml
+include nf_core/.pre-commit-prettier-config.yaml

nf_core/.pre-commit-prettier-config.yaml

@@ -0,0 +1,5 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v2.6.2"
+    hooks:
+      - id: prettier

nf_core/lint_utils.py

@@ -63,7 +63,7 @@ def run_prettier_on_file(file):
         If Prettier is not installed, a warning is logged.
     """
 
-    nf_core_pre_commit_config = Path(nf_core.__file__).parent.parent / ".pre-commit-config.yaml"
+    nf_core_pre_commit_config = Path(nf_core.__file__).parent / ".pre-commit-prettier-config.yaml"
     try:
         subprocess.run(
             ["pre-commit", "run", "--config", nf_core_pre_commit_config, "prettier", "--files", file],
@@ -73,7 +73,11 @@ def run_prettier_on_file(file):
     except subprocess.CalledProcessError as e:
         if ": SyntaxError: " in e.stdout.decode():
             log.critical(f"Can't format {file} because it has a syntax error.\n{e.stdout.decode()}")
-        else:
+        elif "files were modified by this hook" in e.stdout.decode():
+            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():
             log.warning(
                 "There was an error running the prettier pre-commit hook.\n"
                 f"STDOUT: {e.stdout.decode()}\nSTDERR: {e.stderr.decode()}"