Question: Can Supernova run with more than 28 cores?
Answer: The maximum number of CPU that Supernova will use is set at 28 cores. You can raise that to a maximum of 32 using the
--localcores option, but unlike our other software, this is the ceiling for Supernova.
Mainly this is because most of the assembly is done by a series of individual multi-threaded processes. This is in contrast to our other software, which tends to parallelize by spawning multiple independent low thread count jobs. This is why we can get performance gains running Cell Ranger and Long Ranger in cluster mode, but Supernova does not have a cluster mode. It's set up this way because for the most part you can't split up a monolithic assembly job into smaller independent chunks, unlike (for example) aligning reads to a genome, where you can split up the data and process different batches of reads independently.
All that said about Supernova specifically, the pipeline framework (Martian) that all 10x software uses (including Supernova) does not have a limit, but pipeline management operations would be only a small portion of the overall Supernova computation. So you might see short periods where core usage does exceed 32, but this would be Martian, not Supernova proper.
Please consult the Supernova System Requirements for more details.