bdbagFetch.sh

#!/bin/bash

if [ -z "${3}" ]
then
    bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}_inputBag
    for i in $(find */ -name "*R*.fastq.gz")
    do
        path=${2}.$(echo ${i##*/} | grep -o "R[1,2].fastq.gz")
        cp ${i} ./${path}
    done
elif [ "${3}" == "TEST" ]
then
    bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1}
fi