Tests are slow due to too many web queries and limits set by web resources

Description of feature

Many tests will pull form the github repo. 55 in total. This means running the tests once already pulls 55 times, running them repeatedly every couple of minutes over the course of a day apparently isn't well appreciated by github. There are other connections, too, that are done by the tests: refgenie 1x, nf-co.re 12x, api.github.com 1x, pypi.org 2x.

The repeated pulls make the tests slow and repeating the pull can probably be avoided for many tests. One pull, should be enough, and the resulting directory used could e.g. just be copied locally. It would even be nice to have the tests be mostly reduced to local folders. Git supports local repos and as such it might be possible to have the complete test suite contained in this project. After all, if we allow arbitrary git repos, it should not be restricted to repos available over http(s).

There might be some parts of the code that might have to be adapted to allow local folders as resources.

E           git.exc.GitCommandError: Cmd('git') failed due to: exit code(1)
E             cmdline: git pull -v --progress origin
E             stderr: 'fatal: unable to access 'https://github.com/nf-core/modules.git/': Could not resolve host: github.com'

No files, tests, or entry points are named in the issue. Start by locating the tests that access GitHub, refgenie, nf-co.re, the GitHub API, and PyPI, then trace how repository resources are fetched. Done should mean the suite avoids unnecessary repeated remote pulls and can use local repositories or folders where appropriate.