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I'm trying to implement a workflow with GATK for the first time and I'm getting caught out by the -nct/-num_threads options not being compatible with all walkers, erroring and then killing the process.
Can I suggest that if the flags are not implemented/supported by a walker that the option is ignored. The docs don't clarify which walkers work and which don't so I need to test each one. It would be much easier if simply a warning message were given.
Also, I don't fully understand the difference between -nct/-num_threads. Can someone explain it, please?