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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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resources/--j #1065

Closed hanrong498 closed 1 month ago

hanrong498 commented 2 months ago

Hi,

Thanks for the active development of snakePipes :)

I noticed that in the version 3.0.0, there is no longer the option --local and --j. Could you explain how can I allocate more resources to the pipeline now?

Thanks a lot! Hanrong

WardDeb commented 1 month ago

Hi Hanrong,

--local could be replicated by specifying 'shared/profiles/local' as snakemakeProfile under your defaults.yaml file (snakePipes info to retrieve this one). -j within the local configuration can be replicated by setting the cores: flag in the corresponding yaml file (rerunning snakePipes info after setting the profile will give you it's full path).

Number of parallel jobs can be set in non-local jobs by setting the respective flag in your snakemake profile (jobs: )

Hope this helps !

hanrong498 commented 1 month ago

perfect, thanks a lot!