Weakness in current Makefile: as written will happily process the first R1 and R2 fastqs that it finds, ignoring any additional fastqs in dir that are found by the find command. This potentially results in a sample processed using only a subset of its reads, with no indication that anything is wrong.
If there are more than 2 valid fastqs, Makefile should instead crash. (Ideally, process them all; but that is not priority to implement as fab can take care of it.)
Weakness in current Makefile: as written will happily process the first R1 and R2 fastqs that it finds, ignoring any additional fastqs in dir that are found by the find command. This potentially results in a sample processed using only a subset of its reads, with no indication that anything is wrong.
If there are more than 2 valid fastqs, Makefile should instead crash. (Ideally, process them all; but that is not priority to implement as fab can take care of it.)
also minor cleanup: