nf-core_modules/modules/ivar/trim/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_TRIM {
tag "$meta.id"
label 'process_medium'
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publishDir "${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) {
container "https://depot.galaxyproject.org/singularity/ivar:1.3.1--h089eab3_0"
} else {
container "quay.io/biocontainers/ivar:1.3.1--h089eab3_0"
}
input:
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tuple val(meta), path(bam), path(bai)
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path bed
output:
tuple val(meta), path("*.bam"), emit: bam
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tuple val(meta), path('*.log'), emit: log
path "versions.yml" , emit: versions
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script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
ivar trim \\
$options.args \\
-i $bam \\
-b $bed \\
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-p $prefix \\
> ${prefix}.ivar.log
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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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"""
}