For certain tools, like bwa or blast, there is a non-configurable number
of threads to use inside the tool xml.
This is inconvenient for certain cluster configurations, where what we
want is division of a job into multiple jobs (I guess this is what is
intended by the <parallel> tag), and not creation of threads that may
wreak havoc in a cluster.

Is there any reason why bwa and blast have --num-threads=8
pre-configured in the xml file?

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