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Update ivar consensus

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drpatelh 2021-02-23 20:36:03 +00:00
parent f4af709634
commit 9098ba41c8
1 changed files with 1 additions and 1 deletions
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2
software/ivar/consensus/main.nf
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@ -34,7 +34,7 @@ process IVAR_CONSENSUS {
def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : "" def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
""" """
samtools mpileup \\ samtools mpileup \\
--fasta-ref $fasta \\ --reference $fasta \\
$options.args2 \\ $options.args2 \\
$bam | \\ $bam | \\
$save_mpileup \\ $save_mpileup \\