Add threads to snakemake, allow parallel jobs to be launched within thread limit

[lcoombe]

• Set-up snakemake to allow parallel jobs while still adhering to the number of specified threads by the user
• For indexlr jobs, regardless of threads specified, only allow two to run at a time
  • This is to control the memory - since the Bloom filter needs to be loaded for each indexlr job too. When creating the solid BF, we have 2xBF size in memory, so by having this constraint, we will not be ballooning the memory too much
• Also for indexlr jobs, they do not scale past 5 threads, so use this hard threshold for number of threads used for indexlr, regardless of the specified number