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Update software/ivar/consensus/main.nf

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Harshil Patel 2021-02-12 23:02:04 +00:00 committed by GitHub
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software/ivar/consensus/main.nf
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@ -32,7 +32,6 @@ process IVAR_CONSENSUS {
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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 \\ --fasta-ref $fasta \\