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:

    XAVIER/workflow/rules/trim_map_preprocess.smk

    Line 127 in 3feaf86

    samtools sort -@12 -m 4G - -o {output}