I noticed that salmon uses more resources than given with the --threads parameter, i.e. for a value of 10 I observe CPU usage (in top) of 1100%. I guess there are 10 worker threads and one "master" thread?
This is slightly critical on HPC systems where jobs using more resources than requested are killed by the admins.
Maybe it would be sufficient to document this, e.g. "The number of additional threads to use concurrently." (like in samtools).
Wondering what valid values for threads are? What does actually happen if I use 0?