Improving user experience in Snakemake

[icui]

• Determine the right Python version for snakemake, currently the numbering ">=3.12" leads to unexpected behavior
• Snakemake has been very aggressive in changing default behaviors including enforcing -j 1 and changing default scheduler to pulp which does not work on Arm macs without Rosetta and does not make sense for the workflows in benchmarks folder. Maybe to should provide a wrapper command with the recommended parameters.