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Commit c02d977a authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Generalize find fastq after fetch

parent ebab7cd7
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2 merge requests!37v0.0.1,!33Resolve "process_qc"
Pipeline #6841 failed with stages
in 8 minutes and 15 seconds
...@@ -3,9 +3,9 @@ ...@@ -3,9 +3,9 @@
if [ -z "${3}" ] if [ -z "${3}" ]
then then
bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1} bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}
for i in $(find */ -name "*.R*.fastq.gz") for i in $(find */ -name "*R*.fastq.gz")
do do
path=${2}$(echo ${i##*/} | grep -o "\.R.\.fastq\.gz") path=16-TA16$(echo ${i##*/} | grep -o "\.R.\.fastq\.gz")
cp ${i} ./${path} cp ${i} ./${path}
done done
elif [ "${3}" == "TEST" ] elif [ "${3}" == "TEST" ]
......
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