(1) In a ramdisk or on a HDD/SSD, temporary directories and regular files were invented to be used. Pipelines are elegant for problems that fit them. There is no virtue in using a pipeline with programs or formats clearly not designed to be used in a pipeline. (2) Is this a recurring task? or a one-time (or rare) job? If the latter then possibly concocting a robust pipeline may take longer than just working with regular files. If the former then maybe you should consider switching/converting to a storage format that fits your needs better.
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