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Wf restructuring

PIAT LUCIEN requested to merge wf_restructuring into dev

The workflow now use a new version of Snakemake tool for efficiently managing computational resources across multiple nodes using the SLURM executor plugin.

The workflow got simplified by reducing the code size, unifying rules, and improving clarity with better comments and advanced Snakemake functions.

New features got added such as QUAST or RagTag.

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