Switched to nf-core bedtools genome cov scale

            "bedtools/bamtobed": {

                "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"

            },

            "bedtools/genomecov": {

                "git_sha": "e8b33e6eb1be2a03abdd2c06068f9a5cebc02bb4"

            },

            "bedtools/intersect": {

                "git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"

            },

// Import generic module functions

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

params.options = [:]

options        = initOptions(params.options)

process BEDTOOLS_GENOMECOV_SCALE {

    tag "$meta.id"

    label 'process_high'

    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), val(scale)

    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}"

    """

    bedtools genomecov -ibam $bam $options.args -bg -scale $scale \\

    | bedtools sort > ${prefix}.bedGraph

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

    """

}

//

//  Utility functions used in nf-core DSL2 module files

//

//

// Extract name of software tool from process name using $task.process

//

def getSoftwareName(task_process) {

    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()

}

//

// Extract name of module from process name using $task.process

//

def getProcessName(task_process) {

    return task_process.tokenize(':')[-1]

}

//

// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules

//

def initOptions(Map args) {

    def Map options = [:]

    options.args            = args.args ?: ''

    options.args2           = args.args2 ?: ''

    options.args3           = args.args3 ?: ''

    options.publish_by_meta = args.publish_by_meta ?: []

    options.publish_dir     = args.publish_dir ?: ''

    options.publish_files   = args.publish_files

    options.suffix          = args.suffix ?: ''

    return options

}

//

// Tidy up and join elements of a list to return a path string

//

def getPathFromList(path_list) {

    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries

    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes

    return paths.join('/')

}

//

// Function to save/publish module results

//

def saveFiles(Map args) {

    def ioptions  = initOptions(args.options)

    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]

    // Do not publish versions.yml unless running from pytest workflow

    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {

        return null

    }

    if (ioptions.publish_by_meta) {

        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta

        for (key in key_list) {

            if (args.meta && key instanceof String) {

                def path = key

                if (args.meta.containsKey(key)) {

                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]

                }

                path = path instanceof String ? path : ''

                path_list.add(path)

            }

        }

    }

    if (ioptions.publish_files instanceof Map) {

        for (ext in ioptions.publish_files) {

            if (args.filename.endsWith(ext.key)) {

                def ext_list = path_list.collect()

                ext_list.add(ext.value)

                return "${getPathFromList(ext_list)}/$args.filename"

            }

        }

    } else if (ioptions.publish_files == null) {

        return "${getPathFromList(path_list)}/$args.filename"

    }

}

// Import generic module functions

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

params.options = [:]

options        = initOptions(params.options)

process BEDTOOLS_GENOMECOV {

    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']) }

    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(intervals), val(scale)

    path  sizes

    val   extension

    output:

    tuple val(meta), path("*.${extension}"), emit: genomecov

    path  "versions.yml"                   , emit: versions

    script:

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

    def args_token = options.args.tokenize()

    def args       = options.args

    args += (scale > 0 && scale != 1) ? " -scale $scale" : ""

    if (!args_token.contains('-bg') && (scale > 0 && scale != 1)) {

        args += " -bg"

    }

    if (intervals.name =~ /\.bam/) {

        """

        bedtools \\

            genomecov \\

            -ibam $intervals \\

            $args \\

            > ${prefix}.${extension}

        cat <<-END_VERSIONS > versions.yml

        ${getProcessName(task.process)}:

            ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")

        END_VERSIONS

        """

    } else {

        """

        bedtools \\

            genomecov \\

            -i $intervals \\

            -g $sizes \\

            $args \\

            > ${prefix}.${extension}

        cat <<-END_VERSIONS > versions.yml

        ${getProcessName(task.process)}:

            ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")

        END_VERSIONS

        """

    }

}

name: bedtools_genomecov

description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome.

keywords:

    - bed

    - bam

    - genomecov

tools:

    - bedtools:

        description: |

            A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.

        documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html

        licence: ['MIT']

input:

    - meta:

        type: map

        description: |

            Groovy Map containing sample information

            e.g. [ id:'test', single_end:false ]

    - intervals:

        type: file

        description: BAM/BED/GFF/VCF

        pattern: "*.{bam|bed|gff|vcf}"

    - scale:

        type: value

        description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch

    - sizes:

        type: file

        description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column

    - extension:

        type: string

        description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments.

output:

    - meta:

        type: map

        description: |

            Groovy Map containing sample information

            e.g. [ id:'test', single_end:false ]

    - genomecov:

        type: file

        description: Computed genome coverage file

        pattern: "*.${extension}"

    - versions:

        type: file

        description: File containing software versions

        pattern: "versions.yml"

authors:

    - "@Emiller88"

    - "@sruthipsuresh"

    - "@drpatelh"

    - "@sidorov-si"

    - "@chris-cheshire"