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Commit 66591ecd authored by Gervaise Henry's avatar Gervaise Henry :cowboy:
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Fix if not exist in bdbagFetch.sh

parent cf08008a
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3 merge requests!37v0.0.1,!24Develop,!23Resolve "process_RSeQC"
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workflow/scripts/bdbagFetch.sh
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#!/bin/bash #!/bin/bash
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")
...@@ -8,7 +8,7 @@ bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1} ...@@ -8,7 +8,7 @@ bdbag --resolve-fetch all --fetch-filter filename\$*fastq.gz ${1}
path=${2}$(echo ${i##*/} | grep -o "\.R.\.fastq\.gz") path=${2}$(echo ${i##*/} | grep -o "\.R.\.fastq\.gz")
mv ${i} ./${path} mv ${i} ./${path}
done done
elif [ ${3} == "TEST" ] elif [ "${3}" == "TEST" ]
then then
bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1} bdbag --resolve-fetch all --fetch-filter filename\$*.txt ${1}
fi fi
\ No newline at end of file
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