Fix tests after modifying the GitLab org-path to nf-core-test

[mirpedrol]

Follow up from #2228

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

[mashehu]

Do I understand correctly, that we don't need the remove-function anymore, because can handle the conflicts now gracefully?

[mirpedrol]

This remove function was added to avoid errors with the GitLab repo, as the org_path there was also nf-core. Now I changed the org_path to nf-core-test as @anoronh4 suggested, so we don't have to remove the modules :)
I think there are some tests failing still, but will hopefully be easy to fix them.

[codecov]

Codecov Report

Merging #2239 (56a71ed) into dev (6ff6dee) will increase coverage by 0.07%.
The diff coverage is 100.00%.

❗ Current head 56a71ed differs from pull request most recent head 73172ea. Consider uploading reports for the commit 73172ea to get more accurate results

@@            Coverage Diff             @@
##              dev    #2239      +/-   ##
==========================================
+ Coverage   73.05%   73.12%   +0.07%     
==========================================
  Files          77       77              
  Lines        8342     8342              
==========================================
+ Hits         6094     6100       +6     
+ Misses       2248     2242       -6     

Impacted Files	Coverage Δ
nf_core/modules/modules_json.py	80.07% <100.00%> (ø)

... and 2 files with indirect coverage changes

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[anoronh4]

https://github.com/mirpedrol/tools/blob/68019595938e7da13a2db68d41a29d336c5fe237/nf_core/modules/modules_json.py#L428-L442

This code chunk is causing a few tests to fail. Because we now have two org_paths certain discordant states are being caught that maybe shouldn't have passed before. i think we can fix this by simply replacing:

for dir_name in missing_installation[repo][component_type]:
    if component in missing_installation[repo][component_type][dir_name]:

with:

if install_dir in missing_installation[repo][component_type]:
    if component in missing_installation[repo][component_type][install_dir]:

that way we are matching installed components with the corresponding org_paths/repos instead of crossing wires.

[mirpedrol]

Thanks for the suggestion @anoronh4 :)
For some reason, the new modules were not correctly installed in these tests, but they were locally and on Gitpod, so it was very difficult to debug!
Hopefully now everything is passing

[anoronh4]

@mirpedrol interesting, i was able to reproduce the CI errors locally, but only after i cleared a local cache of the modules-test repo ~/.config/nfcore/nf-core/modules-test/ (seems like it didn't like my previously loaded git index). I think we are good to go now!