Fix snakemake aggregate call

[lguerard]

Since the call got updated, this update the snakemake recipe as well.

[quentinblampey]

Hi @lguerard, thanks for the PR. Actually, although deprecated, the CLI still supports gene_column for backward compatibility. That is, if gene_column is provided, it will send a warning and use aggregate_genes = True instead.

So, both works and have the same behavior.

I think I'll update all the configs to use aggregate_genes in the 2.1.0 release, but I'll keep the backward compatibility since some users may still use old config files.

I'll close the issue since it is specific to one config file, but I will keep in mind to update all the config files soon.

[lguerard]

Hi @quentinblampey, that makes sense, thanks! And sorry for the extra work 😅