diff --git a/workflow/scripts/bdbagFetch.sh b/workflow/scripts/bdbagFetch.sh index a5ee2629f395cc9ca3d899042c6e2a079545740d..cdbe8e47f9d8e9fe53ea6f7f475c945fcac56c1b 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 $(find */ -name "*R*.fastq.gz") do - path=16-TA16$(echo ${i##*/} | grep -o "\.R.\.fastq\.gz") + path=${2}$(echo ${i##*/} | grep -o "R[1,2]").fastq.gz cp ${i} ./${path} done elif [ "${3}" == "TEST" ]