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snakemake-workflows / cyrcular-calling

A Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA samples enriched for circular DNA.
https://snakemake.github.io/snakemake-workflow-catalog/?usage=snakemake-workflows/cyrcular-calling
MIT License
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Unexpected keyword template_engine #11

Open alexpmagalhaes opened 7 months ago

alexpmagalhaes commented 7 months ago

Hey,

I am trying to run your snakemake workflow and I am getting at error:

SyntaxError in line 42 of https://github.com/snakemake-workflows/cyrcular-calling/raw/v2.0.0/workflow/rules/datavzrd.smk: Unexpected keyword template_engine in rule definition (datavzrd.smk, line 42)

Can you help?

tedil commented 7 months ago

Which snakemake version are you using? I think I may have forgotten to raise the minimum required snakemake version to 7.0: https://github.com/snakemake-workflows/cyrcular-calling/blob/ccd556ac3e007e1f5ffc039a9c2550b067c27dc3/workflow/Snakefile#L3

alexpmagalhaes commented 7 months ago

Hey,

So I got the same error when I used both versions, 6.15 and 7.32

tedil commented 7 months ago

Hm. Starting with a clean checkout of tag v2.0.0, when I perform a dry-run with snakemake 6.15.5, I get Invalid argument for 'cache:' directive. Only True allowed. To deactivate caching, remove directive. With snakemake 7.32.4, a dry-run does not result in any errors.

dlaehnemann commented 7 months ago

Basically, the template_engine keyword was introduced in snakemake 7.0.0: https://github.com/snakemake/snakemake/pull/1412

So any version higher than that should not throw this error. Are you sure you had the correct version of snakemake present / activated when actually running snakemake?

And if the problem does persist, could you provide a little more context of what you did? So interesting things could be:

  1. How did you install snakemake?
  2. What does snakemake --version give, right before you try running snakemake?
  3. With what exact command do you run snakemake?
  4. Any specifics of your setup, that might be relevant (are you e.g. using a cluster system)?

But these are just off the top of my head -- more info is usually more helpful... ;)