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Setting out based on log directive from snakemake #120

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shashwatsahay opened this issue Nov 27, 2024 · 0 comments
Open

Setting out based on log directive from snakemake #120

shashwatsahay opened this issue Nov 27, 2024 · 0 comments

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@shashwatsahay
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shashwatsahay commented Nov 27, 2024

Is there any drawback to using the following code in slurm-submit.py

this way I can directly set the log file and folder based on the rule's log directive?

is there a reason why this is not the default way?

if "output" not in sbatch_options and "log" not in job_properties and CookieCutter.get_cluster_logpath():
    outlog = joblog.outlog
    log = outlog
    sbatch_options["output"] = outlog
elif "log" in job_properties:
    sbatch_options["output"]=job_properties["log"][0]

if "error" not in sbatch_options and "log" not in job_properties and CookieCutter.get_cluster_logpath():
    errlog = joblog.errlog
    log = errlog
    sbatch_options["error"] = errlog
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