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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shovill-pe CPUs not set in task #485

Closed andrewjpage closed 3 weeks ago

andrewjpage commented 1 month ago

:bug:

:pencil: Describe the Issue

The shovill-pe task doesnt take CPUs as input so defaults to 8, however only 4 are passed in.

Pass in the correct number of CPUs in the task. Run the task and figure out how much RAM is normally used (/usr/bin/time -v cmd). Does it really need 16GB? Does it require a 100GB local disk? How much processing time is used and calculate the utilisation of the CPUs? If its not making use of all 4, adjust the task to use less.