Should we have a test for this?

Not sure if we need a test for that, the issue was mainly that I didn't have into account that someone can specify a container in a different syntax than the nf-core modules template 😓

Codecov Report

Merging #2121 (a85b896) into dev (67e3702) will decrease coverage by 0.03%.
The diff coverage is 57.14%.

@@            Coverage Diff             @@
##              dev    #2121      +/-   ##
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- Coverage   71.43%   71.39%   -0.04%     
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  Files          77       77              
  Lines        8350     8356       +6     
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+ Hits         5965     5966       +1     
- Misses       2385     2390       +5     

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LGTM but have any of us actually tested it on a previously non-compliant but acceptable module?

LGTM but have any of us actually tested it on a previously non-compliant but acceptable module?

I tested one of the modules that only has one container, container "<URL>". This will pass the linting as long as there are <= 2 double quotes. It checks separately the lines that contain docker and singularity containers. If you can think of other formats, we should also test it :)

Only thing I can think of is what happens if the image names are really short and the docker/singularity are on the same line? Actually I think in that case we end up assuming there is only one container per-line and that the line starts with the url 😕
At the least we probably need to document that style if it's (semi?) required.

you can check the deepvariant modules or the gatk4/cnnscorevariants that use only one container and no conda is available

you can check the deepvariant modules or the gatk4/cnnscorevariants

Works for this type of modules 👍

what happens if the image names are really short and the docker/singularity are on the same line?

In that case, it will check the number of double quotes, but only try to connect to the first container it finds. If a module is created with nf-core, even if the containers are short, they will be in two separate lines. For local modules, I will add a warning checking that.