Additional output columns needed for Terra.bio

[jvhagey]

Is your feature request related to a problem? Please describe.
No issues, just need additional information to reduce the need for alternative pipeliens

Describe the solution you'd like

The following columns need to be added to Terra.bio output as requested by @bajwamoneeb (DE PHL)

• amrfinderplus_amr_classes
• amrfinderplus_amr_core_genes
• amrfinderplus_amr_plus_genes
• amrfinderplus_amr_subclasses
• amrfinderplus_stress_genes
• amrfinderplus_virulence_genes
• seqsero2_predicted_serotype

Will be addressed in v2.2.0

[NoForkJustCommit]

@bajwamoneeb just wanted to follow up on this request. Sorry for the delay, I wrote a response and then just realised it isn't posted :( .

I can add the information in these columns, but do you want just a series of genes separated by a , ? Also, for the PLUS genes, stress and virulence genes would be in that column and in their own separate column, is that what you want or do you want to have PLUS genes other than stress and virulence (not sure if anything else is in that) ?

[bajwamoneeb]

Hello, Thanks for the reply! Comma separated is fine. Also you don't need to remove anything from the PLUS column. Also is it possible to add serotype, MLST, and beta-lactam gene columns?

…

-------- Original message -------- From: PHX Dev ***@***.***> Date: 2/13/25 11:30 AM (GMT-05:00) To: CDCgov/phoenix ***@***.***> Cc: Moneeb Bajwa ***@***.***>, Mention ***@***.***> Subject: Re: [CDCgov/phoenix] Additional output columns needed for Terra.bio (Issue #178) @bajwamoneeb<https://github.com/bajwamoneeb> just wanted to follow up on this request. Sorry for the delay, I wrote a response and then just realised it isn't posted :( . I can add the information in these columns, but do you want just a series of genes separated by a , ? Also, for the PLUS genes, stress and virulence genes would be in that column and in their own separate column, is that what you want or do you want to have PLUS genes other than stress and virulence (not sure if anything else is in that) ? — Reply to this email directly, view it on GitHub<#178 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATLIKBTBVVBTXVZHNYRZHXT2PTCDDAVCNFSM6AAAAABTOMSSHSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNJXGE2DEMBQHE>. You are receiving this because you were mentioned.Message ID: ***@***.***> [NoForkJustCommit]NoForkJustCommit left a comment (CDCgov/phoenix#178)<#178 (comment)> @bajwamoneeb<https://github.com/bajwamoneeb> just wanted to follow up on this request. Sorry for the delay, I wrote a response and then just realised it isn't posted :( . I can add the information in these columns, but do you want just a series of genes separated by a , ? Also, for the PLUS genes, stress and virulence genes would be in that column and in their own separate column, is that what you want or do you want to have PLUS genes other than stress and virulence (not sure if anything else is in that) ? — Reply to this email directly, view it on GitHub<#178 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ATLIKBTBVVBTXVZHNYRZHXT2PTCDDAVCNFSM6AAAAABTOMSSHSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNJXGE2DEMBQHE>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[NoForkJustCommit]

Pretty sure we can add everything, but the serotyping as that program is not currently run in phx. We are starting to add in species specific subworkflows (C. diff, S. aureus, E. coli and maybe NTM), but Salmonella isn't on our list of to-dos at the moment because its more of Food-borne issue rather than an HAI. I can ask the group, but that would any additions specific to Salmonella would come post those other organisms that are already in our docket to-do.

[NoForkJustCommit]

Hi @bajwamoneeb what do you want in the MLST column? is it the same as requested here? In terms of the beta-lactam column we already report what gamma found for those, but do you want AMRFinderPlus is finding as well then?