Rewrite modules create repo type check.

[ewels]

As discussed on Slack, it's a fairly frequent problem for users to struggle with creating modules due to:

• not running in the root repo directory
• the automatic detection of repo type not working (eg. custom repos for modules)
• the automatic detection breaking / not working (eg. when we added a main.nf to nf-core/modules)

Here I've introduced more explicit declaration of the repo type:

• Use .nf-core.yml file if we can find it, with repository_type key
• Traverse parent directories to look for this file, reset target directory if found (so that we can run from a nested directory)
• Add command line --repo-type flag to specify repo type if no .nf-core.yml file available

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[grst]

Do we also need to update the pipeline template to add the repository_type flag?

We will definitely need to add this to the modules repo I think.

[ewels]

@grst I did the pipeline template in this PR already: #1391

Yeah I was going to do nf-core/modules after this is merged, but I can make the PR now.

[ewels]

oof, tests were failing because the repo type check function had been copied + pasted at some point, so there were two copies of it with the same name. Condensed to one, hopefully should all work now 🤞🏻