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restore samtools cmd to defaults

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Matthias De Smet 2022-05-11 16:17:30 +02:00 committed by GitHub
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commit c8d3de2ad9
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modules/bowtie2/align/main.nf
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@ -36,7 +36,7 @@ process BOWTIE2_ALIGN {
reads_args = "-1 ${reads[0]} -2 ${reads[1]}"
}
def samtools_command = "samtools view -@ $task.cpus --fast --with-header ${args2} > ${prefix}.bam"
def samtools_command = "samtools view -@ $task.cpus --bam --with-header ${args2} > ${prefix}.bam"
"""