Change sed regex for version reporting in pigz modules

[ljwharbers]

Missing backslash in pigz uncompress stub results in unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException

Simplified sed regex to circumvent the missing/added trailing backslash

PR checklist

Closes #6877

• [ x ] This comment contains a description of changes (with reason).

[fellen31]

Could you add a stub test to this module?

Also, make sure to ask to be added to the nf-core GitHub organisation so you can run the GitHub actions :)

[ljwharbers]

@fellen31 Thanks for the reply.
Diving a bit deeper into the sed logic I believe that it wasn't giving the expected result.

I'm still new to contributing to nf-core, but I'm more than happy to help with adding tests. Could you either point me to some examples of how to add tests for this?

[fellen31]

I'm still new to contributing to nf-core, but I'm more than happy to help with adding tests. Could you either point me to some examples of how to add tests for this?

Sure. You would be adding another test identical the current one but with options "-stub" (also add stub to the name of the test). Afterwards run e.g. nf-test test modules/nf-core/pigz/uncompress/ --profile docker --update-snapshot to generate a new snapshot. This will test the stub part of the module, and should catch errors like the one you reported.

For a simple example: https://github.com/nf-core/modules/blob/3abde3de0970781e8e9aeec3cfeed759008a6ef4/modules/nf-core/unzip/tests/main.nf.test

[ljwharbers]

@fellen31 I think it's all in order now. Except for one linting test failing for a different module. Not sure why/how that get's included in these tests.

Is the typical procedure that I would also fix the linting for that module or is this typically still merged because I did not make any changes to those module files?

Thanks again for pointing me in the right direction!

[fellen31]

No you don't need to fix the others. When you update this branch with the latest master, the other test should not be removed from the list of checks.

There was a problem with GitHub Actions earlier today, maybe something is still not working correctly.

[fellen31]

Or actually, in this case it's because PIGZ_COMPRESS is being used in toffee/irmsd tests. It looks like it should be a simple fix (updating meta.yml to match main.nf), so perhaps you could try to fix in this PR, so we can merge with all green checkmarks.

[ljwharbers]

Looking into tcoffee/irmsd, it needs the added types and descriptions in the yaml file. However, while I can 'guess' the types based on the nextflow code, I have no idea what the descriptions should be.

So perhaps this is better that someone adds it who actually uses this.

[fellen31]

Thanks for adding the stub test, looks good to me! 👍

[fellen31]

Looking into tcoffee/irmsd, it needs the added types and descriptions in the yaml file. However, while I can 'guess' the types based on the nextflow code, I have no idea what the descriptions should be.

So perhaps this is better that someone adds it who actually uses this.

Perhaps guessing a bit is ok here, or maybe @luisas could help. I think the linting has been updated to include more checks since that module was added.

[ljwharbers]

Alright, I've added the types and some general descriptions. Feel free to make adjustments @luisas