Implement kaiju-mergeOutputs

[artur-matysik]

Description of feature

Kaiju profiler offers kaiju-mergeOutputs function to merge Kaiju and Kraken (Bracken?) results (see in Kaiju documentation).
I managed to do that in a very dirty custom way, but it will be great to have this as a native option (+ result passed to taxpasta) if both profilers are enabled.

Thanks for considering!

[jfy133]

Hi @artur-matysik thanks for the suggestion!

Hmm, I'm not sure about this. I don't really like/recommend the idea of merging taxonomic profiles of two different tools into one as they can represent very very different outputs. I think you have to be very very careful with this and should only do this in a very 'experimental' manner outside a 'production' pipeline (if that makes sense).

This would also violate the taxpasta structure I believe.

Thoughts @sofstam @Midnighter ?

[artur-matysik]

This would also violate the taxpasta structure I believe.

No, because output of merged Kaiju and Kraken results is in exact Kaiju format - it requires only KAIJU2TABLE (or similar, forgot the name of the process now) and can be feed directly to taxpasta (and its working fine, done it already for own analysis).

[jfy133]

Sorry - you're correct - not structure, but rather concept.

By that I mean in taxpasta we want one table per tool, as there is then no-way to know (unless you embed this in sample/column names, but that's not something we can 'control' so again risks misleading people if not done properly). But like I said, lets see what the others say :)

[sofstam]

I think we can add the kaiju-mergeOutputs to taxprofiler as optional but I do not really like the idea to give it as input to taxpasta as it involves two profilers-if I understand it correctly.

[Midnighter]

I share @jfy133's concerns. I'm also wondering why/what for do you want this? Can you describe your use-case, please?