This PR adds a Kallisto-specific threads parameter in the single-cell SMART-seq parameters to allow override of THREADS ( -> max_threads) when running Kallisto.
Since in SC we're often running many small quantification jobs I don't see running in single-threaded mode to be a major performance issue.
Kallisto is non-deterministic in multi-threaded mode (even with the default fixed random seed) due to the way reads are selected for fragment length estimation- see https://groups.google.com/forum/#!topic/kallisto-sleuth-users/xa19AYvFjTw.
This PR adds a Kallisto-specific threads parameter in the single-cell SMART-seq parameters to allow override of THREADS ( -> max_threads) when running Kallisto.
Since in SC we're often running many small quantification jobs I don't see running in single-threaded mode to be a major performance issue.