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ctmrbio / BACTpipe

BACTpipe: An assembly and annotation pipeline for bacterial genomics
https://bactpipe.readthedocs.org
MIT License
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SHOVILL process running with default threads 8 #149

Closed boulund closed 3 years ago

boulund commented 3 years ago

It looks like the SHOVILL process doesn't adjust the number of threads according to its environment. It appears to be running with the default settings (i.e. 8 threads) all the time.

https://github.com/ctmrbio/BACTpipe/blob/master/modules/shovill/shovill.nf#L15-L21

We should add --cpus ${task.cpus} to the call to shovill to ensure it optimally uses the resources provided to the process in the different profiles. https://github.com/tseemann/shovill#advanced-options

@emilio-r or @abhi18av could you please get that in there and validate?

abhi18av commented 3 years ago

Good catch @boulund !

I've fixed this in https://github.com/ctmrbio/BACTpipe/pull/150