:green_heart: update code-linting workflow

[bunop]

This PR try to fix issues with linting modules

PR checklist

Closes #8

• [ ] This comment contains a description of changes (with reason).
• [ ] If you've fixed a bug or added code that should be tested, add tests!
• [ ] If you've added a new tool - have you followed the module conventions in the contribution docs
• [ ] If necessary, include test data in your PR.
• [ ] Remove all TODO statements.
• [ ] Emit the versions.yml file.
• [ ] Follow the naming conventions.
• [ ] Follow the parameters requirements.
• [ ] Follow the input/output options guidelines.
• [ ] Add a resource label
• [ ] Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • [ ] PROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd
  • [ ] PROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd
  • [ ] PROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd