Dropdown menu for "List of MLST Schemes"

[ajkarloss]

1. For Ecoli, Camilla wants only Actman not both Actman and Pasteur.

2. We need to add a drop down menu for the manually choose the Scheme for each species (spp projects in VIGASP) and one "All" option for running without a specific scheme.

3. We are not going to rerun MLST for all ecoli. Only for those isolates sequenced after March 2025 by choosing "ecoli_4".
   - We can document the results from "Before-March2025" F. ex: "ecoli" is Actman and "ecoli_2" is Pasteur.

4. Set the automatic pipelines with manually selected scheme for that species from the drop down menu

Jeevan will start adding the drop down menu to the MLST pipeline after the final decisions are made.

[Camilsek]

Context: After updating the MLST database it seems like some E. coli isolates have MLST profiles from the Pasteur schema (ecoli) and some the Actman schema (ecoli_4). I (and maybe others) will easily interpret the MLST results wrongly expecting all E. coli to have sequence type (ST) based on the same MLST schema. Therefore we agreed to lock the automatic pipelines to only one schema (Actman).
For other genus we will also need to look closer into this - but then also need to involve others.

All E. coli ran before the update have an ST based the Actman schema for MLST (previuos update this was called ecoli).
After the update of the MLST database (March 2025), some E. coli have ST based on schema "ecoli" and some have based on "ecoli_4".

Reply to 3. All E. coli ran after the update which have a ST based on "ecoli" needs to be rerun with the locked "ecoli_4" database/schema.

reply to 4. The automated pipeline should be locked with the Actman schema for E. coli (confirm that the correct one then is "ecoli_4")

In the documentation we need a list (or a link to a list) with the reference to each mlst/schema to be able to identify which schema is what.

[ajkarloss]

Thanks Camilla. I will add more issues/tasks for all the points your made.

We had "ecoli" from Actman and ecoli_2 from Pasteur in the previous DB version as well. But we had results only from "ecoli" since it had better similarity to the input genome (build from fastq reads). But in the newerr version, they are similar to Pasteur than Actman.

Is it ok to add which Schema in the down menu? like "ecoli_4-Actman", senterica-MLST, campylobator-MLST, So people know exaclty what they are running instead of checking ?

[karinlag]

Our agreement yesterday was to

1. Keep the naming of the schema as it comes with the mlst tool
2. Show that name in the drop down menu

[ajkarloss]

I remember that. Camilla suggested this because the drop down options will be a longer text. But my suggestion is to show people clearly what they are running exactly (even for us) instead of going to the docunentation to find. But, if you both agree that we dont need to add that info, its fine for me too :)

[Camilsek]

I see your point, @ajkarloss. I will have a short discussion with @karinlag about this before we conclude.

[karinlag]

Just to have things clear @ajkarloss, when it says 'ecoli_4' in the mlst/schema field in the line list, where does that text string come from?