Snakemake slurm cluster status in version 9.6.3

[jessijessi]

Hi everyone,

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 saw that the logger plugins are present but are not working as expected in my system.

I came across the Snakemake SLURM profile repository in this repo, 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.

Thank you in advance,
Best regards

Jessica

[GaspardR]

Hi,

Though I've never tried it, there's the cluster-generic plugin you could try. You would need to write your own submission script, but there's also the option to write your own cluster status script. Hopefully, you can achieve the monitoring you had before.

[jdblischak]

I came across the Snakemake SLURM profile repository in this repo, but it appears that profiles are not compatible with Snakemake versions 8 and above.

The particular profile in this repository is incompatible with Snakemake 8+ (#117)

But I don't see anything in the changelog about deprecating profiles (as of Snakemake 9.13.4), and the documentation still includes instructions on how to use Profiles.

In previous workflows, I relied on version 6, which supported the --cluster, --cluster-status, and --parsable options.

You should be able to use these options with the profile smk-simple-slurm. As of version 2.0.0, it supports Snakemake 8+.

[jessijessi]

Hi,

Though I've never tried it, there's the cluster-generic plugin you could try. You would need to write your own submission script, but there's also the option to write your own cluster status script. Hopefully, you can achieve the monitoring you had before.

Ok, thank you. I will try.

[jessijessi]

I came across the Snakemake SLURM profile repository in this repo, but it appears that profiles are not compatible with Snakemake versions 8 and above.

The particular profile in this repository is incompatible with Snakemake 8+ (#117)

But I don't see anything in the changelog about deprecating profiles (as of Snakemake 9.13.4), and the documentation still includes instructions on how to use Profiles.

In previous workflows, I relied on version 6, which supported the --cluster, --cluster-status, and --parsable options.

You should be able to use these options with the profile smk-simple-slurm. As of version 2.0.0, it supports Snakemake 8+.

Ok, thank you. I will check this things.