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Add function to enable output of mpileup

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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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Anders Goncalves da Silva 2021-02-10 10:02:06 -08:00 committed by GitHub
parent 06770d5f02
commit e9aa037e7b
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1 changed files with 3 additions and 2 deletions
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software/ivar/consensus/main.nf
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@ -28,8 +28,9 @@ process IVAR_CONSENSUS {
path "*.version.txt" , emit: version path "*.version.txt" , emit: version
script: script:
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 |" : ""
""" """
samtools mpileup \\ samtools mpileup \\
-aa -A -d 0 -Q 0 \\ -aa -A -d 0 -Q 0 \\