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Commit 77800005 authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix fastq output name

parent a3839184
2 merge requests!37v0.0.1,!33Resolve "process_qc"
Pipeline #6842 failed with stages
in 8 minutes and 14 seconds
...@@ -5,7 +5,7 @@ then ...@@ -5,7 +5,7 @@ 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 ${i##*/} | grep -o "R[1,2]").fastq.gz path=${2}$.(echo ${i##*/} | grep -o "R[1,2]").fastq.gz
cp ${i} ./${path} cp ${i} ./${path}
done done
elif [ "${3}" == "TEST" ] elif [ "${3}" == "TEST" ]
......
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