Removed local ucsc bedclip module

// Import generic module functions

include { initOptions; saveFiles; getSoftwareName } from './functions'

params.options = [:]

options        = initOptions(params.options)

def VERSION = '377'

process UCSC_BEDCLIP {

    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), publish_id:meta.id) }

    conda (params.enable_conda ? "bioconda::ucsc-bedclip=377" : null)

    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

        container "https://depot.galaxyproject.org/singularity/ucsc-bedclip:377--h446ed27_1"

    } else {

        container "quay.io/biocontainers/ucsc-bedclip:377--h446ed27_1"

    }

    input:

    tuple val(meta), path(bedgraph)

    path  sizes

    output:

    tuple val(meta), path("*.bedGraph"), emit: bedgraph

    path "*.version.txt"               , emit: version

    script:

    def software = getSoftwareName(task.process)

    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"

    """

    bedClip $bedgraph $sizes ${prefix}.bedGraph

    echo $VERSION > ${software}.version.txt

    """

}