Change parallel processing for assemble_reads.py

[bmichanderson]

The previous version of this script would create corescores and coresmemory demands on the system. This change adds an argument --instances that hopefully makes this more explicit.

[bmichanderson]

It seems like (based on my tests on my computer) that the current version of the script will actually create "cores" number of parallel assemblies, each using "cores" cores and "max_memory". This is not what I think makes sense, as it will go way beyond the actual "max_memory" setting and available cores. I've added an argument, "instances" that makes it more explicit. Now, the "cores" argument is per SPAdes assembly, the "max_memory" argument is per SPAdes assembly, and the "instances" determines how many the user wants to run in parallel. The actual demand on the system is "instances" * "cores" and "instances" * "max_memory".

It seems like this is what was perhaps going to be implemented, given "cores" and "max_memory" are passed to the spades_assembly function along with "args", but neither "cores" nor "max_memory" are used in the function (just "args.cores" and "args.max_memory"), leading to the weird behaviour.

There may be other ways to ideally fix this behaviour, so perhaps this pull request is not desired.

Cheers,
Ben