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snakemake / snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster
MIT License
18 stars 19 forks source link

feat: warning if run in job #78

Closed cmeesters closed 4 months ago

cmeesters commented 6 months ago

Already, two issues (#75 and #22) seem to result from running Snakemake in a SLURM job context and using this executor plugin. This PR introduces detecting if triggered within a SLURM job and issuing a warning accordingly.

In principle, the plugin may work in job context. Submitting jobs from jobs has always been a highlight of SLURM. However, settings may lead to unintended behaviour (and would do so without Snakemake, presumably). Hence, we can only warn from the executor.

cmeesters commented 5 months ago

@johanneskoester I think this is a rather trivial change - however, I do not know how to extend the test suite for it. Pointers? Or can it be merged like that?

cmeesters commented 5 months ago

@johanneskoester I consider this an urgent PR - there are always people you try something like this.

cmeesters commented 4 months ago

waited long enough