Be able to run multiple bin QC metrics

[harper357]

Description of feature

I posed this in the slack, but I think it would be great if it was possible to run multiple bin QC metrics (BUSCO, GUNC, CheckM2, etc) and get all of that data in the MultiQC report.

I noticed #707 which adds some new options, but I don't know if it is also allowing for multiple or not.

[jfy133]

I think conceptually this makes sense however it's not so trivial as the output of each one goes into downstream process and possibly a custom script (not written by myself), so it might not be so trivial. It might take a bit of time to get to it

[harper357]

Personally, even if it is just reported in the MultiQC report and not used for anything downstream I think it would be a nice thing to have.

Once the mentioned PR is merged, I can try to work up a new PR to try it out.

Or maybe I should try getting work hours to write up a whole benchmarking pipeline so its easier to compare new software. That seems rather ambitious though.

[jfy133]

So had a chance to quickly through the code:

• One area where we have the one or other for BUSCO/CheckM is filtering contigs for completeness/contamination for going into GTDBTkl but this could then be replaced by parameter to say 'which' of the two outputs should be used for that filtering
• CheckM(1) is required for GUNC (busco doesn't work), but that doesn't block a user from also running BUSCO
• I was mistaken regarding the downstream custom script, that should be fine (BIN_SUMMARY), the script seems to allow inserting all

So actually this might be relatively easy to do in fact (conceptually) ino terms of running everthing :)

However only BUSCO is in MultiQC, so adding CheckM/GUNC etc. into MultiQC is a whole other task 😬

[harper357]

Oh, hmm. Well maybe that is a better use of my time first then.

Thanks for looking into this though!

[jfy133]

Oh, hmm. Well maybe that is a better use of my time first then.

Which bit?

[harper357]

Sorry, I meant writing some MultiQC plugins for CheckM, CheckM2 and GUNC.

[jfy133]

Yes, that would be good! Divide and conquer (at least once I'm not travelling or have sick kids as I now have 😵‍💫🤦🏼‍♀️)