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remove --cluster from v8.x #2866

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conchoecia opened this issue May 8, 2024 · 0 comments
Open

remove --cluster from v8.x #2866

conchoecia opened this issue May 8, 2024 · 0 comments
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enhancement New feature or request

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@conchoecia
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Is your feature request related to a problem? Please describe.
I am trying to troubleshoot a problem that I was having in snakemake 7 where, when I used --cluster "command string here", snakemake would not recognize when target files were present and rules had successfully completed. The same snakemake worked fine when ran without --cluster. I think it is related to #2739 or #2496 . It might be some file latency problem with my SLURM cluster, too.

I switched to snakemake 8 to test my code, and I ran the same command with --cluster. It ran, and I encountered the same issue. I then looked at the documentation for snakemake 8 and realized that --cluster has been replaced with the --executor flag, and the --cluster is no longer supported.

Describe the solution you'd like
I think snakemake 8 should throw an error when --cluster is called and the user should be pointed to the now-supported --executor pattern. If it is deprecated code, maybe that code should also be removed.

Describe alternatives you've considered
The alternative is not doing anything and allowing snakemake to run with the old --cluster instruction. Old scripts may still work, but bug fixes for it would not be supported.

@conchoecia conchoecia added the enhancement New feature or request label May 8, 2024
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