Modules: Have component_files_identical check for new optional files in modules

[asp8200]

#2774

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]

@nf-core-bot changelog

[mirpedrol]

Hello!
I merged #2840 to this branch and modified the code a little bit, I hope it's ok :)
I think applying the patch was working as expected.

What I modified with the last commit is using all files from the modules repo to check if the component files are identical, so we don't need to take into worry about file names in case we have modules with special cases.

The tests were failing because one file from the modules repo didn't exist in the pipeline, which should be considered as False (files are not identical).

[asp8200]

Hello! I merged #2840 to this branch and modified the code a little bit, I hope it's ok :) I think applying the patch was working as expected.

What I modified with the last commit is using all files from the modules repo to check if the component files are identical, so we don't need to take into worry about file names in case we have modules with special cases.

The tests were failing because one file from the modules repo didn't exist in the pipeline, which should be considered as False (files are not identical).

@mirpedrol : Thanks, Juliá. Concerning the failing test: It seems to me that the reason it is failing is that the file environment.yml is missing in the mimic-old-trimgalore, so the linter should fail in that case, right? Should I just adjust the trimgalore-test accordingly?

[mirpedrol]

Concerning the failing test: It seems to me that the reason it is failing is that the file environment.yml is missing in the mimic-old-trimgalore

Checking a bit further on the remaining failing test. We are only installing the module to a pipeline and linting, so it should pass. When I try reproducing this locally, the environment.yml file is modified, because we are now sorting the content of the file alphabetically. I will fix the module in nf-core/modules and hope the test will pass then :)

[asp8200]

Hello! I merged #2840 to this branch and modified the code a little bit, I hope it's ok :) I think applying the patch was working as expected.
What I modified with the last commit is using all files from the modules repo to check if the component files are identical, so we don't need to take into worry about file names in case we have modules with special cases.
The tests were failing because one file from the modules repo didn't exist in the pipeline, which should be considered as False (files are not identical).

@mirpedrol : Thanks, Juliá. Concerning the failing test: It seems to me that the reason it is failing is that the file environment.yml is missing in the mimic-old-trimgalore, so the linter should fail in that case, right? Should I just adjust the trimgalore-test accordingly?

I see. This would have been easy to debug if the test had printed the content of module_lint.failed on fail.

[codecov]

Codecov Report

Attention: Patch coverage is 80.00000% with 2 lines in your changes are missing coverage. Please review.

Project coverage is 74.77%. Comparing base (224c773) to head (848948a).

Files	Patch %	Lines
nf_core/synced_repo.py	80.00%	2 Missing ⚠️

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[asp8200]

@nf-core-bot changelog

[asp8200]

@nf-core-bot changelog