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I am currently using Snakemake version 9.6.3 on a cluster managed by an SLURM scheduler. In previous workflows, I relied on version 6, which supported the --cluster, --cluster-status, and --parsable options. These options have now been deprecated in the newer versions.

I have successfully installed and used the new SLURM executor plugin. However, I noticed that there used to be a way to retrieve the status of all submitted jobs — including whether they completed successfully or failed — using a custom cluster-status script. This functionality was essential for monitoring my workflows, but it is no longer supported in the current version.

I came across the Snakemake SLURM profile repository here: https://github.com/Snakemake-Profiles/slurm, but it appears that profiles are not compatible with Snakemake versions 8 and above.

At this point, I’m unsure how to proceed.

  • Is there an alternative method in Snakemake 9.6.3 to obtain the status of cluster jobs?
  • How can I track whether each job was successful or not?

Any guidance or suggestions would be greatly appreciated.

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  • The documentation here,referenced from where you link, says: "With --seconds-between-status-checks, you set the wait time between rounds of status checks of all submitted jobs." So it should be at least checking on all. This issue dicussion here seems pertinent. Any chance it sparks some commands/options to try? Or here? Commented Oct 20 at 14:22
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