nf-core_modules/modules/rseqc/inferexperiment/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 RSEQC_INFEREXPERIMENT {
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::rseqc=3.0.1 'conda-forge::r-base>=3.5'" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_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"
}
input:
tuple val(meta), path(bam)
path bed
output:
tuple val(meta), path("*.infer_experiment.txt"), emit: txt
path "versions.yml" , emit: versions
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script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
infer_experiment.py \\
-i $bam \\
-r $bed \\
$options.args \\
> ${prefix}.infer_experiment.txt
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(infer_experiment.py --version | sed -e "s/infer_experiment.py //g")
END_VERSIONS
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"""
}