Specify threads/cpus in cluster config

[kelly-sovacool]

• [ ] In each rule, set threads based on cluster config file like here https://github.com/CCBR/RENEE/blob/fb8613b55e3856bf1579ee197d6318e0e325bc18/workflow/rules/paired-end.smk#L57
• [ ] Double-check that all rules that use multithreading/processing use the threads directive in the shell/script/run block. There are currently some instances of samtools -@ being hard-coded. Also look for common flags used by other commands like -t and -p.
  • e.g. known instance here: https://github.com/CCBR/XAVIER/blob/3feaf86c48a0f99c0080eaf31c9742839fce539d/workflow/rules/trim_map_preprocess.smk#L127