Removed local bamtobed module

// Import generic module functions

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

params.options = [:]

options        = initOptions(params.options)

process BEDTOOLS_BAMTOBED {

    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::bedtools=2.30.0" : null)

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

        container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"

    } else {

        container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"

    }

    input:

    tuple val(meta), path(bam)

    output:

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

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

    script:

    def software = getSoftwareName(task.process)

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

    """

    bedtools bamtobed -i $bam $options.args > ${prefix}.bed

    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt

    """

}