Adapt modules install to new directory structure

[ErikDanielsson]

Updated nf-core modules install (and some other stuff...) to accommodate new directory structure, as suggested in #1159:

• Update structure in modules.json to:

...
repos: {
    "repo_owner/repo_name": {
         "module_name": {
              "git_sha": commit_sha
         }
    ...
    } 
    ...
}

• Updated creation of modules.json accordingly.
• Changed default value for since in module_utils.get_module_git_log due to breaking changes in nf-core/modules.
• Changed references to software directory to modules in ModulesRepo.

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

[KevinMenden]

PR looks good, but we'll need to add a few things to get the tests running. I think we can merge once we have the tests for modules install running, and then we can fix the other tests in separate PRs I guess.

You'll need to modify the pipeline template --> simply rename the software into the modules directory for instance. I'll try to think of other changes but maybe you already fixed it now 😅