Fix TEMPLATE branch about hic HOT 3 CLOSED

fixed in 1.2.0dev

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Hi @ewels

I will save some times in the coming days to update nf-core-hic (py2 -> 3).

Regarding the TEMPLATE branch, do I have to manually update it myself and how?

If I create the merge from the current TEMPLATE branch, I guess it will not be up-to-date?

Thanks

from hic.

Hi @nservant,

That's great! This first merge from TEMPLATE to dev is probably going to be pretty painful, with a lot of merge conflicts that you will have to manually resolve and sanity check. It doesn't really matter which template version you do the merge at, as once there is a shared history then the future template updates will be much easier. So to make it as painless as possible, I would make sure that TEMPLATE has the version that is closest to the current status of the main pipeline and do the merge from that. Then update it afterwards.

So, roughly speaking, I guess this is the process:

1. Compare the hic pipeline to the different nf-core template releases and figure out which is closest
2. Update the TEMPLATE branch if necessary to have this version of the template, run with the setup options from the hic pipeline (name, description etc).
3. If you did this on the main nf-core fork, sync everything with your local fork [docs]
4. Run the manual merge process [docs]
5. Push / PR back to the main fork
6. Use the nf-core sync command to update the template to the latest version [docs followed by docs] (again on your fork is safest - remember to push / PR both dev and TEMPLATE branches if done on your fork)

Basically I would start by reading the entire sync documentation page, as you'll be using pretty much all of it 😅

When going through merge conflicts and deciding what is correct, I would recommend referring to the template files (for the relevant version of the template), as seeing that complete pipeline there often clarifies things.

I hope that helps! Shout if you have any questions / ping on Slack. There are quite a few people who have gone through this process now (me, @drpatelh, several others) who should be able to help.

Phil

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