Snakemake: Migrating from deprecated cluster.json to new profiles.yaml
It looks like you can just bundle your cluster config in its own YAML file, and reference that from within a profile YAML.  Here's a clumsy little example using a fake job submission script: https://github.com/ressy/example-snakemake-profiles



The current documentation makes it sound like cluster configuration support is going away and being replaced by profiles:


  While still being possible, cluster configuration has been deprecated by the introduction of Profiles.


...but from those example profiles, that might be misleading; here's an example template for a profile YAML that references a separate cluster-config YAML:

https://github.com/Snakemake-Profiles/generic/blob/master/%7B%7Bcookiecutter.profile_name%7D%7D/config.yaml

...
cluster-config: "$((INSTALDIR))/overwrite_cluster_param.yaml" #abs path
...


That cluster-config YAML has the same default and per-rule entries just your JSON version does:

https://github.com/Snakemake-Profiles/generic/blob/master/%7B%7Bcookiecutter.profile_name%7D%7D/overwrite_cluster_param.yaml

...
# specific parameters for certain rules, which need more time/memory

#run_assembler:
#  queue: bigmem
#  time: 100
#   threads and memory definen in config file


So I think you can just set up a pair of YAML files accordingly including options for your rsem_quantify and star_map_human rules.  From my own test it looks like it handles the cluster argument templating just as it did before when using a profile.  (If this is correct we should nag them to make the new documentation more explicit though.)