Codecov Report

Merging #2090 (69cfe04) into dev (f0b6c48) will decrease coverage by 0.00%.
The diff coverage is 42.85%.

@@            Coverage Diff             @@
##              dev    #2090      +/-   ##
==========================================
- Coverage   68.01%   68.01%   -0.01%     
==========================================
  Files          43       43              
  Lines        5625     5628       +3     
==========================================
+ Hits         3826     3828       +2     
- Misses       1799     1800       +1     

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Hmm I don't think the logic in this command is that solid.

I get the following in my custom repo:

CRITICAL Cannot find directory 'modules/genie/samtools/merge'. Should be TOOL/SUBTOOL or TOOL

The thing is samtools/merge exists on the remote but I removed it and haven't yet pushed that change to the remote.
It also doesn't see a new module I have created but not yet pushed as an option.
This command should (I think) only ever be run in an actual modules repo no? And typically when you are creating a new module and so it won't be in the remote?

So really I don't think it should be using the ModulesRepo at all? It should be deriving the available modules from the actual directory it is in?

I have added a new branch on git-lab called org-path to test these things https://gitlab.com/nf-core/modules-test/-/tree/org-path

I have added a new branch on git-lab called org-path to test these things https://gitlab.com/nf-core/modules-test/-/tree/org-path

Do we need to change the tests in this branch or has a PR been made separately which uses that branch for tests in tools?

we can start in this PR and then migrate some of the other remote-url tests for the other commands in separate PR(s).

Seems to work OK for me!