I am doing the template update right now. I was just wondering whether there is a reason behind the file structure in workflows? If not, I would suggest to include the code in workflows/sra/main.nf directly in workflows/fetchngs.nf.

yeah, we wanted to keep these separate since we have a sra and another workflow

But there is only sra inside of the workflows folder: https://github.com/nf-core/fetchngs/tree/dev/workflows?

oh yeah

So, I will just move everything to workflows/fetchngs.nf from workflows/sra/main.nf, if you are okay with it?!

yes go for it please

Will do, thanks!

Hi. I find https://github.com/nf-core/fetchngs/pull/365 confusing to review because it’s doing multiple things at once. Also, it doesn’t involve a merge commit with the

TEMPLATE

branch, which will make future template upgrades complain about conflicts. I’ve completed the 3.5.1 template upgrade the usual way in https://github.com/nf-core/fetchngs/pull/363 . It’s just merging the new template, solving the conflicts, and updating the tests. Nothing else. I would recommend getting #363 reviewed and merged first. Potentially an upgrade to 3.5.2 quickly done. And then #365 rebased and rebilled as introducing topics and reworking the base workflows.

Thanks @Matthieu Muffato, you’re right, that was my mistake. This is my first time handling a template upgrade, and I bundled too many things into #365 and committed those changes too late. I agree with your proposal. Let’s get #363 merged first, then I’ll rebase #365.

yeah, it looked good enough to me to merge, given the fact that we have another TEMPLATE merge incoming

Thanks @Maxime Garcia

On the contrary, I think we need to solve the 3.5 template now before the 4.0 template kicks in. There are now many merge conflicts with the

TEMPLATE

branch arising from merging #365. I can look into those now

We merged in the 3.5, which I assume is what's creating these merge conflicts

The PR didn’t come from the TEMPLATE branch so it can’t be detected as a template merge

Oh I see. I only looked at the code, and that looked ok to me

I’ve just updated #363

I can have a go tomorrow morning if you don't have time before

Hopefully the tests will pass

Yeah, I got that from time to time

super, thank you Maxime !

Thanks both, and thanks @Matthieu Muffato for the fix! Next time I’ll make sure to merge from the TEMPLATE branch directly so we avoid those conflicts👍