Update/pipeline template 2.10

[anoronh4]

Syncing the pipeline to the nf-core template pipeline to make sure it is compatible with nf-core tools 2.10 and current with the latest nf-core standards.

[github-actions]

Python linting (black) is failing

To keep the code consistent with lots of contributors, we run automated code consistency checks.
To fix this CI test, please run:

• Install black: pip install black
• Fix formatting errors in your pipeline: black .

Once you push these changes the test should pass, and you can hide this comment 👍

We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

Thanks again for your contribution!