Add support for generic git remotes

[ErikDanielsson]

Until now, we have used the GitHub API to work with remote modules repositories. As is outlined in #1626, this limits the possible git remotes to GitHub. In this PR I have rewritten how we handle git remotes in the modules commands to work with any remote that works with command line git. This works by cloning the remote repositories into the .nfcore directory. When running modules command, we run git pull on all repositories that are affected by the command.

Outline of changes

• To support any git remote the --github-repository option is changed to --git-remote, and the argument should be a valid git URL.
• Added --no-pull flag to nf-core modules. This allows the user to run a modules command without pulling the remote repository.
• The structure of the modules.json file is changed to keep track of the git URL. Hence, I have update the pipeline template. The new structure is as follows

{
    "name": "some name"
    "homePage": "https://some_page.com"
    "repos": {
        "path/in/git/remote": {
             "git_url": "git@git_provider.com:path/in/git/remote.git",
             "modules": {
                 "very-nice-module": {
                     "git_sha": "some hex"
                 },
                 ...
             }
         },
         ...
     }
}

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

[codecov]

Codecov Report

Merging #1641 (c558fd3) into dev (67fae3b) will increase coverage by 0.45%.
The diff coverage is 48.76%.

@@            Coverage Diff             @@
##              dev    #1641      +/-   ##
==========================================
+ Coverage   64.39%   64.84%   +0.45%     
==========================================
  Files          54       54              
  Lines        6299     6270      -29     
==========================================
+ Hits         4056     4066      +10     
+ Misses       2243     2204      -39     

Impacted Files	Coverage Δ
nf_core/modules/module_test.py	48.27% <ø> (ø)
nf_core/modules/test_yml_builder.py	48.62% <ø> (+0.22%)	⬆️
nf_core/modules/update.py	7.81% <0.00%> (+0.06%)	⬆️
nf_core/__main__.py	51.68% <14.81%> (+0.90%)	⬆️
nf_core/modules/module_utils.py	34.40% <25.00%> (-3.20%)	⬇️
nf_core/modules/info.py	20.58% <28.57%> (+1.49%)	⬆️
nf_core/modules/modules_command.py	52.53% <29.16%> (-5.68%)	⬇️
nf_core/lint/modules_json.py	78.26% <50.00%> (-6.74%)	⬇️
nf_core/modules/modules_repo.py	75.33% <74.30%> (+1.46%)	⬆️
nf_core/modules/lint/module_changes.py	87.50% <75.00%> (+11.50%)	⬆️
... and 8 more

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[ewels]

Clone progress bar: use percentage for progress, more colour on the left and a rich URL to make it a clickable link for the remote.

[ewels]

LGTM 🦜