Template: correctly strip .R -R common extensions
Template: correctly strip .R -R common extensions

Correctly handles initial fastq naming using alternatives to _R1
naming. Thanks to @vbarrera

biocyberman/bcbio-nextgen,biocyberman/bcbio-nextgen,chapmanb/bcbio-nextgen,a113n/bcbio-nextgen,vladsaveliev/bcbio-nextgen,lbeltrame/bcbio-nextgen,chapmanb/bcbio-nextgen,biocyberman/bcbio-nextgen,vladsaveliev/bcbio-nextgen,chapmanb/bcbio-nextgen,vladsaveliev/bcbio-nextgen,a113n/bcbio-nextgen,lbeltrame/bcbio-nextgen,lbeltrame/bcbio-nextgen,a113n/bcbio-nextgen