Bioinformatics workflows for genomic characterization, submission preparation, and genomic epidemiology of pathogens of public health concern.
GNU General Public License v3.0
33
stars
15
forks
source link
[TheiaProk] tbprofiler optimizations #427
Open
kapsakcj opened 2 months ago
:cool:
:pushpin: Explain the Request
tb-profiler runs single-threaded, despite WDL task requesting 8 CPUs
https://github.com/theiagen/public_health_bioinformatics/blob/2f1b35163126571e3f349707fd64efeb1aee348f/tasks/species_typing/mycobacterium/task_tbprofiler.wdl#L18
Need to add
--threads ~{cpus}and we could consider--ram ~{memory}to limit max RAM usage.We should also consider upgrading to the latest version of tb-profiler. The current version as of today is v6.2.0 and the default is v4.4.2
:books: Context
:chart_with_upwards_trend: Desired Behavior
:information_source: Additional Information