diff --git a/workflow/scripts/bdbagFetch.sh b/workflow/scripts/bdbagFetch.sh index 0bf20f0354ff7403a1a783a93c7e3f10b5bb35bb..606b88397d5a6cf4feb4aa38d7615e3e3ba48735 100644 --- a/workflow/scripts/bdbagFetch.sh +++ b/workflow/scripts/bdbagFetch.sh @@ -5,7 +5,7 @@ then bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1} for i in $(find */ -name "*R*.fastq.gz") do - path=${2}.$(echo ${i##*/} | grep -o "R[1,2]").fastq.gz + path=${2}.$(echo ${i##*/} | grep -o "R[1,2].fastq.gz") cp ${i} ./${path} done elif [ "${3}" == "TEST" ]