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snakemake / snakemake-executor-plugin-slurm

A Snakemake executor plugin for submitting jobs to a SLURM cluster
MIT License
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Wildcards missing from comments #85

Closed mrvollger closed 1 month ago

mrvollger commented 2 months ago

Hello,

I was very excited to see in the patch notes the inclusion of wildcards in the slurm comment and log path.

So I updated the plugin to get those features, and while I see wildcards in the log path (e.g. .snakemake/slurm_logs/rule_fire/PS00474_HG02630_1_JAHAOQ010000001.1/18033650.log), I still don't see them in the SLURM comment field, just the rule name (e.g. fire). Any ideas?

Thanks in advance, Mitchell

cmeesters commented 2 months ago

Hello Mitchell,

yes, indeed. We could do that. At first I was a bit hesitant - not knowing what the buffer size for SLURM strings is. And I bloody well do not want to break anybodies batch system. Yet, SLURM matured over time and as far as I can tell (please, anyone correct me, if I am wrong!), there is no such string limit for comments of job names. And my own tinkering with hello world scripts confirms this.

So, I will - as time permits - draft a PR.

Cheers Christian

mrvollger commented 1 month ago

Great! Made a small PR ^. Hope it helps.

mrvollger commented 1 month ago

closed in #88.

cmeesters commented 1 month ago

Ah, you are faster than me - got pretty busy.

Anyway, this issues does not go without a "Thank you!".