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Add reference fasta as input

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Anders Goncalves da Silva 2021-02-12 11:26:55 -08:00
parent 6b22bb9782
commit a4bba006bd
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software/ivar/consensus/main.nf
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@ -20,6 +20,7 @@ process IVAR_CONSENSUS {
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam)
path(fasta)
output: output:
tuple val(meta), path("*.fa") , emit: fasta tuple val(meta), path("*.fa") , emit: fasta
@ -33,6 +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
-aa -A -d 0 -Q 0 \\ -aa -A -d 0 -Q 0 \\
$options.args2 \\ $options.args2 \\
$bam | \\ $bam | \\