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I say that as somebody who (in my very un-humble opinion) is highly proficient at using make, and with a vast experience writing NGS pipelines using make: I did it all through my PhD and postdoc, and I also used the GNU make-based iRAP pipeline which was developed by a colleague (and for which I provided extensive testing and feedback).
NOTE:
The number of mentions on this list indicates mentions on common posts plus user suggested alternatives.
Hence, a higher number means a more popular project.