diff --git a/workflow/scripts/bdbag_fetch.sh b/workflow/scripts/bdbag_fetch.sh index 117340ba29c690915ff15209036c091698cc90b7..761b9c3971276de7ad39258c1832dca8b2ce87a3 100644 --- a/workflow/scripts/bdbag_fetch.sh +++ b/workflow/scripts/bdbag_fetch.sh @@ -2,15 +2,7 @@ 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[1,2].fastq.gz") - cp ${i} ./${path} - done -elif [ "${3}" == "TEST" ] -then - bdbag --materialize ${1} --debug + bdbag --materialize ${1} --debug validateError=true bdbag --validate full ${1} && validateError=false if validateError @@ -27,4 +19,12 @@ then then exit 1 fi + 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 --validate structure --validate-profile ${1} --debug fi