Snakemake version >=6.5 does not schedule jobs optimally

[pontushojer]

This issue was observed for the rule map_sort_ema_bins. It uses 4 cores per job so when 20 cores are available on a node one would expect 5 parallel jobs being running. However instead only one job is run at the time leaving 16 cores unused. I am not sure what the sources of the issue is but it seems that something in the snakemake scheduler was updated that causes this issue.

Tested snakemake versions which show the problem: v6.5.0, v6.5.1, v6.5.2, v6.5.3, v6.6.1, v6.8.1

The latest tested version that worked as expected was v6.4.1.

Issue copied from FrickTobias/BLR#244