From 87b040e122f477551e5d9137a024ba4783046fce Mon Sep 17 00:00:00 2001 From: E-T-K Date: Mon, 17 Oct 2022 12:21:31 -0700 Subject: [PATCH] improve R1/R2 detection in Makefile (#18) --- Makefile | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/Makefile b/Makefile index acd3934..7ab3606 100755 --- a/Makefile +++ b/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"