UCSC-Treehouse / pipelines

Makefiles to run dockerized pipelines used in Treehouse on a single sample
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Makefile: should crash when finding N>2 fastq files #21

Open e-t-k opened 5 years ago

e-t-k commented 5 years ago

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: