Add deprecation notice

[nictru]

As discussed in the #scflow slack channel, this PR adds a deprecation notice to the Repo Readme.

I did not find any good examples in other archived pipelines since the archiving adds similar notices. An example can be found here

[github-actions]

YAML linting 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 yaml-lint
  • Install npm then install yaml-lint (npm install -g yaml-lint)
• Fix the markdown errors
  • Run the test locally: yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")
  • Fix any reported errors in your YAML files

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

We highly recommend setting up yaml-lint 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!

[github-actions]

Markdown linting 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 markdownlint-cli
  • On Mac: brew install markdownlint-cli
  • Everything else: Install npm then install markdownlint-cli (npm install -g markdownlint-cli)
• Fix the markdown errors
  • Automatically: markdownlint . --fix
  • Manually resolve anything left from markdownlint .

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

We highly recommend setting up markdownlint 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!

[maxulysse]

@nf-core-bot fix linting pretty please 🙏

[nictru]

Do we still have to make sure the CI passes in this situation?

[maxulysse]

Do we still have to make sure the CI passes in this situation?

not really, but I like nice things