mlst: new String output "ts_mlst_allelic_profile"

theiagen / public_health_bacterial_genomics

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mlst: new String output "ts_mlst_allelic_profile" #209

Closed kapsakcj closed 1 year ago

kapsakcj commented 1 year ago

~~Setting as a draft until testing in Terra is complete~~

Ready for review

This PR:

adds a new String output to the ts_mlst task called ts_mlst_allelic_profile which is a comma-separated list of genes
- E. coli ST11 example: adk(12),fumC(12),gyrB(8),icd(12),mdh(15),purA(2),recA(2)
adds this new output to both TheiaProk_Illumina_PE and TheiaProk_Illumina_SE workflows
adds this new output to the export_taxon_tables task

Testing on Terra:

[x] ILMN PE
[x] ILMN SE

kapsakcj commented 1 year ago

Tested great in Terra on a handful of samples, but would be good for others to test too.

Only change necessary is to select the cjk-mlst-profile dev branch and to click USE DEFAULTS on the outputs tab for the new output column.

ILMN PE test: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/curtis_sandbox/job_history/d2168efd-94dd-42ba-abb8-013a795ab6fa

ILMN SE test: https://app.terra.bio/#workspaces/cdph-terrabio-taborda-manual/curtis_sandbox/job_history/d2168efd-94dd-42ba-abb8-013a795ab6fa

cimendes commented 1 year ago

Tested on Terra.bio, LGTM!

kapsakcj commented 1 year ago

Emma & Inês - Thanks for testing. I'd prefer to keep the mlst output TSV for consistency sake - since folks are used to having that file available, I'd prefer to keep it as an output