Check 'modules' directory structure

[mirpedrol]

Add a step in all nf-core modules commands to check if the modules directory of a pipeline has the correct structure. See slack discussion

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

[ewels]

Reading the code looks good 👍🏻

[ewels]

Can we not just git pull update it? 👀

[mirpedrol]

I did it like this in case there is a patch file

[ewels]

This is the cached modules repo though, right? ~/.config/nfcore/nf-core/modules/?

Patch files are held in the pipeline repo, so the central cache location should be unaffected by those.

[mirpedrol]

Oh yes you are right, I mixed things.
So for this I copied code from you 😇 from #1851
But if there's a better way of doing it, let's change!

[ewels]

Yeah but #1851 was for a modules clone that is corrupted, so no git operations would work.

Here the git repo is presumably just behind, so doing a git pull should fix stuff, right? I think the code in self.modules_repo.setup_local_repo() should already be pulling the latest changes:

tools/nf_core/modules/modules_repo.py

Lines 182 to 195 in 227e400

	# If the repo is already cloned, fetch the latest changes from the remote
	if not ModulesRepo.local_repo_synced(self.fullname):
	pbar = rich.progress.Progress(
	"[bold blue]{task.description}",
	rich.progress.BarColumn(bar_width=None),
	"[bold yellow]{task.fields[state]}",
	transient=True,
	disable=hide_progress,
	)
	with pbar:
	self.repo.remotes.origin.fetch(
	progress=RemoteProgressbar(pbar, self.fullname, self.remote_url, "Pulling")
	)
	ModulesRepo.update_local_repo_status(self.fullname, True)

Is this not already working? If so it could be because it's doing git fetch rather than git pull. In other words, it's not checking out the latest commit, it's only downloading them 🤔 I don't think that there's any reason not to change this to a pull...

[codecov]

Codecov Report

Merging #1867 (16d3909) into dev (227e400) will decrease coverage by 0.04%.
The diff coverage is 60.46%.

@@            Coverage Diff             @@
##              dev    #1867      +/-   ##
==========================================
- Coverage   64.49%   64.44%   -0.05%     
==========================================
  Files          34       35       +1     
  Lines        4137     4180      +43     
==========================================
+ Hits         2668     2694      +26     
- Misses       1469     1486      +17     

Impacted Files	Coverage Δ
nf_core/modules/info.py	16.54% <0.00%> (-0.12%)	⬇️
nf_core/modules/modules_command.py	73.73% <39.13%> (-10.48%)	⬇️
nf_core/lint/modules_structure.py	88.88% <88.88%> (ø)
nf_core/modules/test_yml_builder.py	49.54% <100.00%> (+0.22%)	⬆️

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[ewels]

Can probably refine the clone update code instead of deleting and redownloading, but can leave that to another day.