Add sourmash as a profiler (or similar)

[jfy133]

Description of feature

Example workflow: https://taylorreiter.github.io/2022-07-28-From-raw-metagenome-reads-to-phyloseq-taxonomy-table-using-sourmash-gather-and-sourmash-taxonomy/

[jfy133]

@Midnighter has already added some sourmash modules: https://github.com/nf-core/modules/blob/master/modules/sourmash/sketch/main.nf

[vmikk]

Sourmash module PR from Taylor Reiter: nf-core/modules#2176
(not merged yet)

[vmikk]

For taxonomy profiling, we need a new module sourmash/gather (nf-core/modules#2214)

[vmikk]

sourmash/gather should be working now (nf-core/modules#2250).
Now it's the turn for the sourmash/taxonomy module.

[hkaspersen]

Hello! I was wondering if you had a timeline for adding sourmash to Taxprofiler? I am very interested in trying it!

[jfy133]

@vmikk is this still possible on your end, or would you like someone else to take over?

[vmikk]

Hello!
I'm heavily engaged with my day job at the moment and unfortunately, I can't dedicate the necessary time to this project now.
I apologize for any inconvenience caused by this delay.
If quick completion is required, it would probably be more efficient if someone else could step in for now.

However, I've registered for the upcoming hackathon in Barcelona with the hope that it could provide an opportunity for me to finalize this task. I'm optimistic that the focused environment and collective energy at the event will allow me to make significant progress on this.

[jfy133]

OK thanks for the update @vmikk ! We are about to release 1.1 anyway so I don't think sourmash will be fit in there in time.

If there are any taxprofiler devs in BCN maybe you can sit with them @vmikk and power through it! (I won't be there this year due to parental leave).

[jfy133]

@vmikk I've removed you for now as I guess you're still very busy. Feel free to pick this up at a future date if you get time again @:)