document --threads --hapog-threads

[alpapan]

Could we please have some documentation on what these variables actually do?
It will help figure out the right settings for an HPC environment

[bistace]

Hello,

those basically do what the -h says:

  --threads THREADS, -t THREADS
                        Number of threads (used in BWA, Samtools and Hapo-G)
  --hapog-threads HAPOG_THREADS
                        Maximum number of Hapo-G jobs to launch in parallel (Defaults to the same value as --threads)

--threads is given to BWA/Minimap2 as -t and Samtools as -@. --hapog-threads is the number of Hapo-G processes that will run at the same time.