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

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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process IVAR_VARIANTS {
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)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0"
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} else {
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container "quay.io/biocontainers/ivar:1.3.1--h089eab3_0"
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}
input:
tuple val(meta), path(bam)
path fasta
path gff
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output:
tuple val(meta), path("*.tsv") , emit: tsv
tuple val(meta), path("*.mpileup"), optional:true, emit: mpileup
path "versions.yml" , emit: versions
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script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def save_mpileup = params.save_mpileup ? "tee ${prefix}.mpileup |" : ""
def features = params.gff ? "-g $gff" : ""
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"""
samtools mpileup \\
$options.args2 \\
--reference $fasta \\
$bam | \\
$save_mpileup \\
ivar variants \\
$options.args \\
$features \\
-r $fasta \\
-p $prefix
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cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//')
END_VERSIONS
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"""
}