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cover all use cases

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MaxUlysse 2022-06-03 15:37:10 +02:00
parent f1a5cc07db
commit f9ac4e28e9
1 changed files with 1 additions and 5 deletions
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6
modules/tiddit/sv/main.nf
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@ -26,11 +26,7 @@ process TIDDIT_SV {
def prefix = task.ext.prefix ?: "${meta.id}"
def reference = fasta ? "--ref $fasta" : ""
"""
for i in `ls ${bwa_index}`
do
ln -s ${bwa_index}/\$i ${fasta}.\${i##*.}
done
[[ -d $bwa_index ]] && for i in `ls $bwa_index`; do [[ -f $fasta && ! "\$i" =~ .*"$fasta".* ]] && ln -s $bwa_index/\$i ${fasta}.\${i##*.} || ln -s $bwa_index/\$i \$i; done
tiddit \\
--sv \\