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Update modules/bowtie2/align/main.nf

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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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Matthias De Smet 2022-05-11 13:57:27 +02:00 committed by GitHub
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commit 971a889e2a
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modules/bowtie2/align/main.nf
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@ -42,7 +42,7 @@ process BOWTIE2_ALIGN {
"""
INDEX=`find -L ./ -name "*.rev.1.bt2" | sed "s/.rev.1.bt2//"`
[ -z "\$INDEX" ] && INDEX=`find -L ./ -name "*.rev.1.bt2l" | sed "s/.rev.1.bt2l//"`
[ -z "\$INDEX" ] && echo "BT2 index files not found" 1>&2 && exit 1
[ -z "\$INDEX" ] && echo "Bowtie2 index files not found" 1>&2 && exit 1
bowtie2 \\
-x \$INDEX \\