Setting jobs in profiles to use all available cores

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Issue #1305 closed
Michael DePalatis created an issue

I am testing out Snakemake profiles and would like to specify the number of jobs to be the same as the number of available cores. When using command-line arguments, I would be able to do this:

snakemake -j

and Snakemake will determine the right number of cores to allocate. If I instead of a profile/config.yaml file that looks like

jobs:

I get this error:

snakemake: error: argument --cores/--jobs/-j: invalid int value: 'None'

Is there a way to get the behavior of simply passing -j while using profiles?

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