Snakemake: Combine cluster profile with resources: attempt

Question

Let's say I have a rule that for 90% of my data needs 1h, but occasionally needs 3h. In a busy cluster environment, I however do not want to submit all jobs with a time limit of 3h to be save, as this would slow down the scheduling of my jobs.

Hence, I played around with the attempt variable:

resources:
    # Increase time limit in factors of 1h, if the job fails due to time limit.
    time = lambda wildcards, input, threads, attempt: int(60 * int(attempt))

(one could be even smarter and use powers of 2 to amortize better...).

But this approach forces me to put the base time (1h) direclty into the rule. How can I combine this approach with cluster profiles, where the base time is in some cluster_config.yaml file?

Thanks and so long Lucas

question from:https://stackoverflow.com/questions/66059332/snakemake-combine-cluster-profile-with-resources-attempt

Answer 1

Waitting for answers