nf-core_modules/modules/paraclu/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process PARACLU {
tag "$meta.id"
label 'process_low'
publishDir "${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']) }
conda (params.enable_conda ? "bioconda::paraclu=10" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/paraclu%3A10--h9a82719_1"
} else {
container "quay.io/biocontainers/paraclu:10--h9a82719_1"
}
input:
tuple val(meta), path(bed)
val(min_cluster)
output:
tuple val(meta), path("*.bed"), emit: bed
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def VERSION=10
"""
awk -F "\t" '{print\$1"\t"\$6"\t"\$2"\t"\$5}' < $bed > ${bed}_4P
sort -k1,1 -k3n ${bed}_4P > ${bed}_4Ps
paraclu $min_cluster ${bed}_4Ps > ${prefix}.clustered
paraclu-cut ${prefix}.clustered > ${prefix}.clustered.simplified
awk -F '\t' '{print \$1"\t"\$3"\t"\$4"\t"\$1":"\$3".."\$4","\$2"\t"\$6"\t"\$2}' ${prefix}.clustered.simplified > ${prefix}.clustered.simplified.bed
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: $VERSION
END_VERSIONS
"""
}