improve R1/R2 detection in Makefile (#18)

Makefile

@@ -3,8 +3,9 @@
 # Generates expression, fusions, and variants folders in outputs
 
 # Look for any files with 1 or 2 followed by any non-numeric till the end
-R1 = $(shell find samples -iregex ".+1[^0-9]*$$" | head -1)
-R2 = $(shell find samples -iregex ".+2[^0-9]*$$" | head -1)
+# Alternatively, look for R1_001.fastq.gz and R2 -- most common format we use.
+R1 = $(shell find samples -iregex ".+\(1[^0-9]*\|R1_001.fastq.gz\)$$" | head -1)
+R2 = $(shell find samples -iregex ".+\(2[^0-9]*\|R2_001.fastq.gz\)$$" | head -1)
 
 REF_BASE ?= "http://hgdownload.soe.ucsc.edu/treehouse/reference"