Enhancement : update MLST - eventually allow several MLSTs runs

[evezeyl]

Hi,
Now bigsdb/pubMLST has been updated, and at least now the Listeria_2 scheme is the one to use in MLST software. So we can update the image

Also, I was considering the option to add serotyping by MLST as I do in the proficiency test, which basically would mean adding the scheme.
So basically we could allow MLST to run with different schemes. I have an idea (and an example how this could easily be implemented).

• if not specified, run as usual, if several schemes need to be used (several MLST runs) then schemes to be used can be given in a list, comma separated (cf - diplotopia example for bacta params) - so this would mean modifying a bit the channel before MLST and maybe slightly MLST module.
• I would need to create an layer on the latest docker image for MLST to add the scheme (at least the Listeria serotyping scheme) but can add others also if we want.

This would allow doing fast analyses for ringtest (as long as VIGAS-P is not all top notch) and also for any other project (eg. requests and outbreaks where people want MLST and serotyping)

What do you think?

Would you also want eg, additional schemes to be implemented ?

If its ok with you, I can do things, you can crosscheck.?

Eve

[hkaspersen]

Sounds like a good idea!
Not sure if we should add schemas to the image though, as other people might be using it. But adding the schemas as a list and passing them to the mlst process should be relatively easy to implement.
Feel free to create a pull request to the dev branch with an example so I can test the functionality!