skip VADR task if a certain number of Ns are present in consensus assembly

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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skip VADR task if a certain number of Ns are present in consensus assembly #15

Closed kapsakcj closed 3 years ago

kapsakcj commented 3 years ago

Jobs are failing VADR task due to consensus assemblies with too many Ns. Therefore a sample fails completely and no results are populated to the Terra data table.

Would be nice if we could see the results from tasks that did succeed (even if the assembly is 💩 , it might be nice to have)

I'd say this is low priority, but having it would allow for a larger % of jobs to succeed (despite having a poor quality assembly)

kapsakcj commented 3 years ago

This has been occurring for me in Titan PE and Titan SE workflows (don't run ClearLabs or ONT ever)

kevinlibuit commented 3 years ago

Addressed https://github.com/theiagen/public_health_viral_genomics/commit/2ccb2e17e95d562ce38e61eb680ee6b8a15e3cc5