Hardcoded language for seq_method

theiagen / public_health_viral_genomics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of viral pathogens of concern, especially SARS-CoV-2

https://public-health-viral-genomics-theiagen.readthedocs.io/

GNU Affero General Public License v3.0

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Hardcoded language for seq_method #78

Closed frankambrosio3 closed 2 years ago

frankambrosio3 commented 2 years ago

The current default value for seq_method is not an allowed value in the controlled vocabulary for that field and should be switched to "ILLUMINA"

kapsakcj commented 2 years ago

Is this also true for Titan_ClearLabs workflow? Should it be changed to OXFORD_NANOPORE? (just basing off of Frank's Terra metadata formatter & drop-down for "Platform")

https://github.com/theiagen/public_health_viral_genomics/blob/87ca249b440097c1288c8c7de1b851fdc9b1fa6d/workflows/wf_titan_clearlabs.wdl#L19

And Titan_ONT workflow?

https://github.com/theiagen/public_health_viral_genomics/blob/87ca249b440097c1288c8c7de1b851fdc9b1fa6d/workflows/wf_titan_ont.wdl#L18