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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: will reject jobs, which attempt setting job names by 'slurm_extra' #93

Closed cmeesters closed 5 months ago

cmeesters commented 6 months ago

Occasionally, users reported that their attempt to overwrite SLURM job names leads to faulty behaviour (job status does not get queried properly, and a workflow will stall). This is understandable from the code and documented accordingly.

The PR checks for the job status using a regex - simple string matching might be too error-prone (e.g. "-J" can be part of a wildcard).

The decision is here, that the workflow will abort (raising WorkflowError and explaining and pointing to the docs).

Please check whether this is "likeable".

I do not know how to implement a test. The other executors leave me clueless.

cmeesters commented 5 months ago

Please check whether this is "likeable".

Don't think the change is so severe. Please let me know what you think.

fgvieira commented 5 months ago

Yeah, hard to make a testcase but changes not too drastic. Looks good!