Hello people, it's still the "old" Einar, but I forgot to migrate my account to the new work address, so here I am... Would this be a good place to discuss whether some stuff should or should not go into sarek?

Do you need help migrating your old slack account? You know you can change email

If you want to change your email address, got to: http://my.slack.com/account In the top right, select the right workspace. More details here: https://slack.com/help/articles/207262907-Change-your-email-address

My old email is no longer working since a month - oops - so hard to do that 😉

No worries, we can still help out

np!

Give me 5 to arrive at a computer

but yes the right place

Ok, let's then get into that business 😉 Remember that proposal I made a long time ago about a sWGS pipeline? You might also remember a more recent proposal about a newer one... We're trying to merge things, but I do wonder if these pipelines can be put into sarek: the consensus was that one would try, but while not technically against it there a few pain points: • Development surface: even if off and on, getting that PureCN PR in the half-broken state I had took quite an effort, because there are a lot of moving parts • CRAM native (is this still a thing?), can be very problematic with sWGS tools that expect (mainly) BAMs only • Applications outside the scope of sarek (at the moment):; possibly CNV detection in plasma samples (cfDNA) All of this is debatable and could be wrong, but I think that given the state now, it would be a bit hard to push for inclusion in Sarek (I could if I were at my old job but I'm doing something different now so I can't guess how much dev time I could spare). So, are there still strong arguments for keeping a sWGS in sarek, or if it really needs to go in, how can this be made a little simpler?

by sWGS, you mean something like very low coverage?

Yeah, 0.1X-1X

Ok, back with my "real me", so the discussion can actually be productive now 🙂

There was a proposal for shallowseq: https://github.com/nf-core/proposals/issues/127 I think we can have a separate pipeline given the specifities. You seemed involved in the comments, and ready to collaborate, no?

I am, in fact

For me as long as can collaborate as much as possible to avoid duplication and lower maintenance burden, I am happy with a separate pipeline, as it is slightly out of scope in my opinion