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[TheiaProk] tbprofiler optimizations #427

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kapsakcj opened this issue Apr 19, 2024 · 0 comments · May be fixed by #673
Open

[TheiaProk] tbprofiler optimizations #427

kapsakcj opened this issue Apr 19, 2024 · 0 comments · May be fixed by #673
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🆒

📌 Explain the Request

tb-profiler runs single-threaded, despite WDL task requesting 8 CPUs

public_health_bioinformatics/tasks/species_typing/mycobacterium/task_tbprofiler.wdl

Line 18 in 2f1b351

Int cpu = 8

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

📚 Context

📈 Desired Behavior

ℹ️ Additional Information
@sage-wright sage-wright changed the title tbprofiler optimizations [TheiaProk] tbprofiler optimizations Apr 24, 2024
@sage-wright sage-wright self-assigned this May 6, 2024
@sage-wright sage-wright mentioned this issue May 6, 2024
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@sage-wright sage-wright linked a pull request Nov 8, 2024 that will close this issue
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