don't update modules_json if module is not updated

[mirpedrol]

Close #2014

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• 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

[mirpedrol]

Hi @ewels, I opened this PR to fix #2014, here I remove the piece of code which updates the modules_json object when we don't update the module but only show the differences or write them on a file.

The bug in this issue was happening because when we preview differences for all modules, we can choose to not update a module, but the modules_json object is updated anyway, if we do update another module, when we dump the changes in modules_json to the file the previous changes are also duped.

I remember I tried to remove this piece of code a while ago, and you told me it wasn't a good idea, but I can't see a case where we would want to update modules_json if the module is not updated. Am I missing something? Or is this a remnant from old code and can be safely removed?

[codecov]

Codecov Report

Merging #2323 (fbe8155) into dev (37c3d06) will decrease coverage by 0.02%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##              dev    #2323      +/-   ##
==========================================
- Coverage   72.86%   72.84%   -0.02%     
==========================================
  Files          78       78              
  Lines        8774     8773       -1     
==========================================
- Hits         6393     6391       -2     
- Misses       2381     2382       +1     

Impacted Files	Coverage Δ
nf_core/components/update.py	80.98% <ø> (-0.05%)	⬇️

... and 1 file with indirect coverage changes

[mashehu]

Did we change something in the update function that it now writes a file or why does this solve the problem?

[mirpedrol]

I think this bug has always been there, but we only see it if we update all modules, decide not to update one of them, and then continue updating the rest. Because we will change the sha value for the not updated one and write it to the file while updating the others afterwards.