nf-core_modules/modules/ivar/consensus/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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process IVAR_CONSENSUS {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::ivar=1.3.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0"
} else {
container "quay.io/biocontainers/ivar:1.3.1--h089eab3_0"
}
input:
tuple val(meta), path(bam)
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path fasta
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output:
tuple val(meta), path("*.fa") , emit: fasta
tuple val(meta), path("*.qual.txt"), emit: qual
tuple val(meta), path("*.mpileup") , optional:true, emit: mpileup
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path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
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"""
samtools mpileup \\
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--reference $fasta \\
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$options.args2 \\
$bam | \\
$save_mpileup \\
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ivar consensus \\
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$options.args \\
-p $prefix
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echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//' > ${software}.version.txt
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"""
}