Running Snakemake on a slurm queue, ctrl+C does not kills submitted job

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Issue #1301 new
Colin Brislawn created an issue

I’m not sure if this is a known limitation or considered out of scope for snakemake.

After pressing ctrl+C, I was expecting snakemake to send a ‘scancel’ command to SLURM before shutting itself down. It looks like snakemake just allows all queued jobs to finish.

It’s also possible that I’m overlooked the documented way to address this, so any feedback you have is much appreciated.

Related issues:

https://bitbucket.org/snakemake/snakemake/issues/298/when-running-snakemake-as-a-subprocess https://bitbucket.org/snakemake/snakemake/issues/773/snakemake-tries-to-resume-a-slurm-job-that#comment-53564426

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