nf-core_modules/software/rseqc/bamstat/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
def options = initOptions(params.options)
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process RSEQC_BAMSTAT {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::rseqc=3.0.1" : null)
if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/rseqc:3.0.1--py37h516909a_1"
} else {
container "quay.io/biocontainers/rseqc:3.0.1--py37h516909a_1"
}
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input:
tuple val(meta), path(bam)
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output:
tuple val(meta), path("*.bam_stat.txt"), emit: txt
path "*.version.txt" , emit: version
script:
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def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
bam_stat.py \\
-i $bam \\
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$options.args \\
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> ${prefix}.bam_stat.txt
bam_stat.py --version | sed -e "s/bam_stat.py //g" > ${software}.version.txt
"""
}