Added bedtools sort

//

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    // Do not publish versions.yml unless running from pytest workflow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

    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(bed)

    val   extension

    output:

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

    path  "versions.yml"                   , emit: versions

    script:

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

    """

    bedtools \\

        sort \\

        -i $bed \\

        $options.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_sort

description: Sorts a feature file by chromosome and other criteria.

keywords:

    - bed

    - sort

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/sort.html

        licence: ['MIT']

input:

    - meta:

        type: map

        description: |

            Groovy Map containing sample information

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

    - bed:

        type: file

        description: Input BED file

        pattern: "*.{bed}"

output:

    - meta:

        type: map

        description: |

            Groovy Map containing sample information

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

    - bed:

        type: file

        description: Sorted BED file

        pattern: "*.{bed}"

    - versions:

        type: file

        description: File containing software versions

        pattern: "versions.yml"

authors:

    - "@Emiller88"

    - "@sruthipsuresh"

    - "@drpatelh"