new module: RGI/AUTOLOAD

louperelo commented 1 year ago

Is there an existing module for this?

[X] I have searched for the existing module

Is there an open PR for this?

[X] I have searched for existing PRs

Is there an open issue for this?

[X] I have searched for existing issues

Are you going to work on this?

[X] If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module

apalleja commented 6 months ago

Hi @louperelo and @mirpedrol!

I am participating in the nf-core hackathon 2024. I would like to see if I can contribute in solving this issue. I have used RGI from CARD some times, but I am a beginner in nf-core. Please let me know if you can explain me the issue and if you think I can contribute, I am not sure of the level of difficulty.

Albert

mirpedrol commented 6 months ago

Hi @apalleja, sorry for the late reply. You can definitely contribute :) I couldn't find a module rgi/autoload so feel free to take over. The issue is referring to creating a new module using this tool. I don't know the tool, but if you have used it before that's perfect.

jasmezz commented 6 months ago

Hey everyone, the reason for this issue was the RGI update 5 from to 6. This apparently introduced a new way of handling the CARD database within the RGI tool, so we (or rather @louperelo) thought of bundling all commands in a new rgi/autoload module. I tackled this issue already and think it's the best way to have one module for each rgi command: rgi card_annotation to prepare a downloaded CARD database to load into RGI. The subsequent commands rgi load and rgi main are then included in the rgi/main module (we cannot have them separately). Both modules exist already. The only thing missing would be an rgi/download module. As you can see in the main.nf.test file, we solved this until now with a one-liner. But it wouldn't harm to have it wrapped in a separate module.

nf-core / modules