Hello, Adding a new module, but I'm getting pre-commit errors:

git commit -m "add module bamixchecker"
[WARNING] The 'rev' field of repo '<https://github.com/nf-core/tools>' appears to be a mutable reference (moving tag / branch).  Mutable references are never updated after first install and are not supported.  See <https://pre-commit.com/#using-the-latest-version-for-a-repository> for more details.  Hint: `pre-commit autoupdate` often fixes this.
Sort dependencies in conda environment files...............................................Passed
prettier...................................................................................Passed
Match meta.ymls in one of the subdirectories of modules/nf-core............................Failed
- hook id: check-jsonschema
- exit code: 1

Error: schemafile could not be parsed as JSON
SchemaParseError: /home/abenjak/Projects/nf-core/BAMixChecker/modules/modules/yaml-schema.json
  in "/home/abenjak/.cache/pre-commit/repoo3ir6trd/py_env-python3.13/lib/python3.13/site-packages/check_jsonschema/checker.py", line 56
  >>> return self._schema_loader.get_validator(

  caused by

  FailedFileLoadError: Failed to parse /home/abenjak/Projects/nf-core/BAMixChecker/modules/modules/yaml-schema.json
    in "/home/abenjak/.cache/pre-commit/repoo3ir6trd/py_env-python3.13/lib/python3.13/site-packages/check_jsonschema/schema_loader/readers.py", line 27
    >>> schema = callback()

    caused by

    JSONDecodeError: Expecting value: line 1 column 1 (char 0)
      in "/home/abenjak/.cache/pre-commit/repoo3ir6trd/py_env-python3.13/lib/python3.13/site-packages/check_jsonschema/parsers/__init__.py", line 92
      >>> return loadfunc(data)

      caused by

      StopIteration: 0
        in "/home/abenjak/miniconda3/envs/nfcore/lib/python3.13/json/decoder.py", line 361
        >>> obj, end = self.scan_once(s, idx)

Validate environment.ymls against schema...................................................Passed
Match meta.ymls in one of the subdirectories of subworkflows/nf-core...(no files to check)Skipped
Validate GitHub Workflows..............................................(no files to check)Skipped
ruff...................................................................(no files to check)Skipped
ruff-format............................................................(no files to check)Skipped
Check .editorconfig rules..................................................................Failed
- hook id: editorconfig-checker
- exit code: 1

modules/nf-core/bamixchecker/tests/main.nf.test:
	No final newline expected

1 errors found

Lint Dockerfiles.......................................................(no files to check)Skipped
Lint nf-core subworkflows..............................................(no files to check)Skipped

Tried from scratch with all nf-core versions from

2.14.1

to

3.2.0

, with or without

pre-commit autoupdate

. The first error regarding

yaml-schema.json

was already reported in a comment above. The second error

No final newline expected

is wrong because everything is fine with my

main.nf.test

(to make sure, I also tried using

main.nf.test

from another recent module, and it fails the same way).

regarding the first fail, can you try linking the file

yaml-schema.json

to

meta-schema.json

? as suggested before

it doesn't work. softlink

yaml-schema.json

to meta-schema.json:

ln -sf meta-schema.json modules/yaml-schema.json
ll modules/yaml-schema.json
lrwxrwxrwx 1 abenjak 16 2025-03-17 09:54 modules/yaml-schema.json -> meta-schema.json

but the same error occurs. There are no final new lines in the

main.nf.test

. And I get the same newline error if I try with any other

main.nf.test

from another module. (also in case someone wonders, I'm on Linux, there are no CR LF in my files).

can you try committing with the option

--no-verify

and open a PR? that way the tests will run in our runners and you will be able to share the code so we can have a look