def VERSION = '10' // Version information not provided by tool on CLI process PARACLU { tag "$meta.id" label 'process_low' conda (params.enable_conda ? "bioconda::paraclu=10" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/paraclu%3A10--h9a82719_1' : '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 args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ 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 > ${prefix}.clustered.simplified.bed cat <<-END_VERSIONS > versions.yml "${task.process}": paraclu: $VERSION END_VERSIONS """ }