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nf-core

Hi modules team,
I am working on a Parabricks starfusion module. All the test data already exists on `nf-core/test-datasets` except the `<http://AnnotFilterRule.pm|AnnotFilterRule.pm>`. I submitted a <https://github.com/nf-core/test-datasets/pull/1752|PR> into the test data repo to add this file.

You know, you make a good point :sweat_smile: This is an interesting case then. The module I'm building requires starfusion build as a pre-processing step. And similar to the last Parabricks module I wrote, I had to package an older version for compatibility. The issue is in that accessory module's test (<https://github.com/clara-parabricks-workflows/nf-core-modules/blob/72c25c3ed49bf2d8b99267cf0529e94aa11cfc4f/modules/nf-core/parabricks/starfusion/tests/main.nf.test#L87|see here>). It points to a URL that is not in the test-modules repo. <@U065DAZ0PL5> for viz

I guess my real question is, is it okay to have this file exist outside the test data repo? Or is there some alternative I should pursue?

I am wondering whether this file is needed only for the test

or whether its something that is utilized somewhere else and why there is a script being imported as an input (it all confuses me)

I did some research and it seems to be a Perl module script with filtering and annotation rules. It's typically a local file, but this module test is pointing to a version hosted by the broad.

I'm a bit at a loss for how to proceed and now my PR is in limbo. If I shouldn't proceed with uploading this file to the test-data repo, then how should I proceed? <@UE6D8290F>

Straight from the <https://github.com/TrinityCTAT/ctat-genome-lib-builder/wiki#installing-a-ctat-genome-lib-data-resource|CTAT lib documentation>, the `<http://AnnotFilterRule.pm|AnnotFilterRule.pm>` file is required as input to the `prep_genome_lib.pl` function. Since we can't have it locally in the nftests, I'm proceeding with the <https://github.com/nf-core/test-datasets/pull/1752|PR> for adding this to the test data repo.

Let's do whatever is necessary to get your stuff going, and we can always improve on it later

Sorry for taking so long to get back to you

That's okay! You are very busy and I appreciate your time!