slurm - Snakemake delete output files from master node if cluster job gets killed

Question

I am running snakemake on the login node of a cluster using the slurm job queuing system.

Unfortunately, if a slurm job times out, or if it gets killed with scancel, the snakemake script inside the job does not delete the output files, since it gets killed as well.

The master snakemake process however stays alive in these circumstances, so I would like this process to delete the output files of the failed child jobs. Is there an option for that, or some hack that does this?

question from:https://stackoverflow.com/questions/65937444/snakemake-delete-output-files-from-master-node-if-cluster-job-gets-killed

Answer 1

Waitting for answers