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vinisalazar / metaphor

Metaphor: a general-purpose workflow for assembly and binning of metagenomes
https://metaphor-workflow.readthedocs.io/
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configuring threads/cores in local run #53

Closed Perugolate closed 1 year ago

Perugolate commented 1 year ago

When running metaphor locally, what is the best way to set the number of threads available to snakemake?

I am able to configure the RAM but not the threads when I configure the settings via:

metaphor config settings

When running metaphor execute, then snakemake seems to default to 4 cores:

Snakemake will start with 4 cores

Apologies if I missed in the documentation.

vinisalazar commented 1 year ago

Dear @Perugolate,

The recommended way is to set the number of threads with the -c command-line option. This is by design as Snakemake itself requires the number of cores to be specified in the command-line (with the same -c option).

Best, Vini