Backlog PRs from the release block for review pretty please please: • github.com/nf-core/sarek/pull/2401/changes (template update, if someone can double check the rocrate update) • github.com/nf-core/sarek/pull/2402 Add Deepsomatic model ffpe. • github.com/nf-core/sarek/pull/2395/changes Trigger tests of the corresponding modules config changes • github.com/nf-core/sarek/pull/2391/changes Make lane optional in samplesheets collected the last three in a stack so they can go in at once: github.com/nf-core/sarek/stack/2404 I will then review these: • github.com/nf-core/sarek/pull/2389 Controlfreec without sex information • github.com/nf-core/sarek/pull/2161/changes xengsort And work on: • github.com/nf-core/sarek/pull/2392 think about the lower case PR. It’s more tricky than I thought. • github.com/nf-core/sarek/pull/2353 Wrap up the PB haplotypefiltering.

https://github.com/nf-core/sarek/pull/2400/ is closed already

ah sorry wrong link I had accidentally opened it from my fork and then moved. correct link is in the stack. and here: github.com/nf-core/sarek/pull/2402

stack was closed when I checked

I had an idea regarding the FFPE

replied. Tl;dr: deepsomatic is the only one with an FFPE mode. I checked all other callers

I think for freebayes we could for example adjust the standard settings a bit more based on that

we don’t generate the PON so whatever people do there in #C05GH685FKJ is out of our control. I don’t see any guidance in the freebayes docs: github.com/freebayes/freebayes do you have more info there?

freebayes docs are horrible 😞

What do you want to do in createpanelrefs?

you are on your own I think 😆

We could add such a flag if there something that exist

I am doing some lookup with gemini into FFPE optimization and I just think we can do better and apply it where we think it fits

ok let me know what you find. my stance is generally to be fairly careful with changing the default parameters unless there is an explicit call out from the tool developers for certin scenarios

I just did a very brief sweep nothing conclusive yet and I understand your hesitation but I think having the ffpe flag would make sense since its so widely used and I just do not want to add this singular flag only to remove it later? Maybe it also makes sense to have the type of sample prep in the sample sheet (not sure abou that though). But also its a #C078586GZ5X and i think you can go ahead for now since its pretty clear for deepsomatic

can you please have your agent add the sources where this information is retrieved from

yes I will spend some more time on that to be conclusive 🙂 so from my side good to go for now

I can let this PR be for a few days, I should try to merge it by tuesday latest

I will not have enough time until then 🙂 I would say go ahead and if I find somethinhg we discuss it later

ok let’s leave for monday meeting to discuss though

Sounds good

will remove it from the list so the rest can get in