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marbl / verkko

Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
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Snakemake 8 compatibility #224

Open tbenavi1 opened 8 months ago

tbenavi1 commented 8 months ago

Hello,

I recently updated my version of Snakemake to version 8, and now Verkko doesn't work. Specifically, I get the following error:

snakemake: error: unrecognized arguments: --reason

According to https://github.com/snakemake/snakemake/blob/main/docs/getting_started/migration.rst, "--reason" is deprecated since it is always true now.

Would it be possible to update Verkko to work with Snakemake 8? Thanks so much.

skoren commented 8 months ago

No plans in the short term (next few months). Snakemake 8 is a major breaking change (like python 3 vs 2) and so, if we support it the users on snakemake 7 would be unable to run verkko. I expect there to still be more users of snakmake 7 than 8 so when we do upgrade I'd hope verkko to detect/use both. For now, I recommend sticking with snakemake 7 and/or using a conda environment to use snakemake 7 for verkko.

skoren commented 6 months ago

When running on python3.12, there are errors w/invalid escape characters and finally an error with the constructed resource strings:

/home/runner/work/verkko/verkko/lib/verkko/Snakefiles/c1-buildStore.sm:55: SyntaxWarning: invalid escape sequence '\`'
  # make sure we weren't given compressed read
...
Select jobs to execute...
InputFunctionException in rule buildStore in file /home/runner/work/verkko/verkko/lib/verkko/Snakefiles/c1-buildStore.sm, line 19:
Error:
  KeyError: ' sto _mem_gb '
Wildcards:

Would make sense to address this when we update to Snakemake 8.