theiagen / public_health_bioinformatics

Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
GNU General Public License v3.0
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Reduce Gambit task resource requirements #489

Closed andrewjpage closed 3 months ago

andrewjpage commented 4 months ago

:bug:

:pencil: Describe the Issue

Gambit is very efficient with its resource usage.

Modify the task resources to 1 CPU, 2 GB RAM and 20 GB local disk. Modify the task to pass in the number of CPUs. Test this works.

This task runs for an average of 6 seconds. Make it preemptible (spot) so that we can access lower pricing. Google give 30 seconds notice before killing it, so we shouldn't notice any difference.

In the runtime section of the task set:

maxRetries: 3
preemptible: 1