Improve documentation for using nf-core/tools for external pipelines/customizing it during development

[FriederikeHanssen]

Is your feature request related to a problem? Please describe.
At the moment, there seems to be no concise guide on how to use nf-core/tools for custom pipelines and how to deal with the various components.

This page is touching on what to update in the documentation and removing the .github files. But it is placed under guidelines. While developing a pipeline I find it more natural to check somewhere where also the remaining developmental steps are explained.

There is also this guide under he tools documentation for removing components while creating the pipeline https://nf-co.re/docs/nf-core-tools/pipelines/create#customization . Also not the first place I would check during development, since my pipeline was already created.

Describe the solution you'd like
A collection of resources could be a good start on what to do when you develop a pipeline outside of nf-core.

Describe alternatives you've considered
A new guide may duplicate information and get out of sync. The documentation around customizing the create command should really stay with tools