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epi2me-labs / wf-single-cell

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Time directives for all processes #115

Closed WardDeb closed 5 months ago

WardDeb commented 5 months ago

Hello,

I'm running wf-single-cell on an HPC system that requires walltime set for submission (via slurm). I could set a general time for all the processes but I think it makes more sense to have process specific walltimes (as overestimation would result in waiting time penalties). This PR sets some ballpark figures for time estimates for all processes. These shouldn't affect 'local' runs, though I haven't got the means to really test this.

Kind regards,

WardDeb

nrhorner commented 5 months ago

Hi @WardDeb

Thanks for the PR. I don't think time declarations are something we'd want to bake into the processes, and we'd probably want to leave this up to users sort out.

You could achieve the same result with process selectors: https://www.nextflow.io/docs/latest/config.html#process-selectors.

for example

process {
    withName: assign_barcodes {
        time "08:00:00"    
    }
}

Thanks,

Neil

WardDeb commented 5 months ago

Fair enough, thanks for the pointers !

Kind regards,

WardDeb