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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 13:59:03 +02:00 committed by GitHub
parent 9097abf277
commit bcd7fe55b1
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modules/bowtie2/align/main.nf
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@ -51,7 +51,7 @@ process BOWTIE2_ALIGN {
$unaligned \\ $unaligned \\
$args \\ $args \\
2> ${prefix}.bowtie2.log \\ 2> ${prefix}.bowtie2.log \\
| ${samtools} | $samtools_command
if [ -f ${prefix}.unmapped.fastq.1.gz ]; then if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz