bdbagFetch.sh

#!/bin/bash

if [ -z "${3}" ]
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.\.fastq\.gz")
        mv ${i} ./${path}
    done
elif [ "${3}" == "TEST" ]
then
    bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1}
fi