Hi, I found this PR ,dealing with TMB, is already merged github.com/nf-core/modules/pull/9660#… but it was not added to the nf-core modules so far. Does anybody know when is it planned to do so? Thanks

what do you mean? I see it here: https://github.com/nf-core/modules/tree/master/modules/nf-core/tmb/pytmb

oh, sorry, I checked sarek repo, so the modules are not updated there, is that right?

pytmb is not part of sarek at the moment in general. there were some efforts in the past but noone followed through so far. (not opposed to having it, just need someone that puts some energy behind it)

I see, and would be too complicated to add it? Because it would make the analysis easier to have it in one go 🙂 I mean, I could try, if you think it is possible

I have tried here: github.com/nf-core/sarek/pull/616/changes#… but lost momentum. (That PR is probably beyond rescue, but maybe the discussion underneath helps). Looking at it it doesn't look too difficult

ok, I can see that it was 4yrs ago, I thought that now, when it is finally the part of nf-core modules, it should be much easier to implement it, but maybe I am wrong

I think I got stuck here github.com/nf-core/sarek/pull/616#… If you are using the tool, maybe you have some insights. I also wanted to make it picture perfect so users would not need to supply the resource files. I have come around now to better have the tool there and users need to supply everything, then get stuck by trying to get all resource files pre-set

Alright, so I will take a look, I am little bit lost since I didn't follow the PR from the beginning, but it would be worth to trying Do you have any suggestions what where to start? with removing normalisation from it?

yep I am trying to merge in dev now. Then I think in some order: • swap out the local module for the nf-core module • maybe remove the existing subworkflow, and put the tmb module into the existing postvariantcalling on at the appropriate position • Review the assets • write up some docs, metromap etc

ok, thank you! let me know, when you finish merging😉

Merged: github.com/nf-core/sarek/pull/616/changes#… but there are changes that need to be removed like the lib/.groovy file. Up to you if you just want to open a fresh PR and link the two PRs

I'm sorry, but it is not merged in the dev, is it?

no it needs much cleaning before merging in

so the easiest way will be to merge your PR into my branch and than start a new PR, I suppose

no we can't merge that one into dev, it will break everything. I think the easiest will be if you create a new Pr from dev and use the existing one for inspiration but otherwise jsut implement the tmb module

okay, so I'll start the new one and will see how it goes :)

sounds good