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settable pod5, samtools and modkit optimization parameters

Carlos Gomes requested to merge dev/optm-sam-modkit into main
  • fix #4
  • adds new runtime settable parameters for pod5, modkit and samtools that can be used to configure maximize resource usage—namely, cpu and mem
  • the default values were taken from the existing ones, except for the threads, which is usually twice the existing one (this is safe)
  • updated all workflows and processes by adding any new parameters to the end of the flow/process input
  • updates the documentation with the new parameters

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