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Hello! I'm working on modules for SUPPA. However I have some questions about the test data. Some modules would require specific files generated by the tool, and I'm not sure how/where/if those should go into the modules test-data. Anyone who can guide me through this please? Thanks!

Does this draft page help? 

<https://github.com/nf-core/website/pull/4283|https://github.com/nf-core/website/pull/4283>

(Just needs a final review from <@U024MM1DRKL> to go in)

Otherwise the test data specs are here: <https://nf-co.re/docs/specifications/test-data/overview|https://nf-co.re/docs/specifications/test-data/overview>

But if neither of these help feel free to post questions here :) (you looking through the docs will be helpful and we can improvement if it's still unclear ;))

Thanks! I've seen it but I couldn't find the convention of the folder structure for files generated by downstream processes. I feel that the idea is to use setup instead and use the existing modules starting from the generic test data?

I've seen your PR and it shows the actual expected structure. I think that's an important piece of information missing (I think) from current docs. I'll try to avoid pushing new test-data by using the setup phase of tests.

&gt; Thanks! I've seen it but I couldn't find the convention of the folder structure for files generated by downstream processes.
&gt; 
I'm not sure I follow here...

&gt;  I feel that the idea is to use setup instead and use the existing modules starting from the generic test data?
&gt; 
But generally yes we prefer to just build the input from upstream modules when it is very fast to do so, or the needed input files are larger than the GitHub repo file size limit.

Then try to reuse or create files based on existing rest data on the repo from the 'generic' stuff (e.g. SARS-CoV-2)

And the finally if nothing else is really possible you can put very specific tool specific files under the `delete me` folder

Looking at my specific case, I'm developing a module for `suppa.py psiPerEvent` <https://github.com/comprna/SUPPA#psi-calculation-for-transcripts-and-events|github.com/comprna/SUPPA#…> which expects an expression file in tpm units plus the events generated by suppa itself (already added that module to nf-core). I'm looking for an expression matrix now.

ok, found this
SRP254919.salmon.merged.gene_counts.top1000cov.tsv: Count matrix derived by running rnaseq workflow against the mouse genome GRCm38 with default parameters

I'll try to reuse everything avail, in the extreme case, I'll upload to delete me. Thanks for helping!

Sorry - I have seem this! It's on my Monday list to review. I don't expect many changes from my quick check on my phone