Merge pull request #79 from Functional-Genomics-Lab/bedtools-general

Bring bedtools up to speed

.github/filters.yml

@@ -144,3 +144,27 @@ trimgalore:
 ucsc_bedgraphtobigwig:
   - software/ucsc/bedgraphtobigwig/**
   - tests/software/ucsc/bedgraphtobigwig/**
+
+bedtools_complement:
+  - software/bedtools/complement/**
+  - tests/software/bedtools/complement/**
+
+bedtools_genomecov:
+  - software/bedtools/genomecov/**
+  - tests/software/bedtools/genomecov/**
+
+bedtools_intersect:
+  - software/bedtools/intersect/**
+  - tests/software/bedtools/intersect/**
+
+bedtools_merge:
+  - software/bedtools/merge/**
+  - tests/software/bedtools/merge/**
+
+bedtools_slop:
+  - software/bedtools/slop/**
+  - tests/software/bedtools/slop/**
+
+bedtools_sort:
+  - software/bedtools/sort/**
+  - tests/software/bedtools/sort/**

software/bedtools/complement/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/bedtools/complement/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BEDTOOLS_COMPLEMENT {
+    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(beds), path(sizes)
+
+    output:
+    tuple val(meta), path('*.complement.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 \\
+        complement \\
+        -i $beds \\
+        -g $sizes \\
+        $options.args \\
+        > ${prefix}.complement.bed
+
+    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    """
+}

software/bedtools/complement/meta.yml

@@ -0,0 +1,59 @@
+name: bedtools_complement
+description: Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file.
+keywords:
+    - bed
+    - complement
+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/complement.html
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - beds:
+        type: file
+        description: List of bed files
+        pattern: "*.{bed}"
+    - sizes:
+        type: file
+        description: File which defines the chromosome lengths for a given genome
+        pattern: "*.{sizes}"
+
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bed:
+        type: file
+        description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
+        pattern: "*.{complement.bed}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    -"@Emiller88"
+    -"@sruthipsuresh"

software/bedtools/genomecov/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/bedtools/genomecov/main.nf

@@ -0,0 +1,40 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def 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), 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(bams)
+
+    output:
+    tuple val(meta), path("*.bed"), emit: coverage
+    path  "*.version.txt", emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    bedtools \\
+        genomecov \\
+        -ibam $bams \\
+        $options.args \\
+        > ${prefix}.bed
+
+    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    """
+}

software/bedtools/genomecov/meta.yml

@@ -0,0 +1,58 @@
+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
+
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: List of bam files
+        pattern: "*.{bam}"
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bed:
+        type: file
+        description: Computed genomecov bed file
+        pattern: "*.{bed}"
+
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+
+authors:
+    -"@Emiller88"
+    -"@sruthipsuresh"

software/bedtools/intersect/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/bedtools/intersect/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BEDTOOLS_INTERSECT {
+    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(bed1), path(bed2)
+
+    output:
+    tuple val(meta), path('*.intersect.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 \\
+        intersect \\
+        -a ${bed1} \\
+        -b ${bed2} \\
+        $options.args \\
+        > ${prefix}.intersect.bed
+
+    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    """
+}

software/bedtools/intersect/meta.yml

@@ -0,0 +1,59 @@
+name: bedtools_intersect
+description: allows one to screen for overlaps between two sets of genomic features.
+keywords:
+    - bed
+    - intersect
+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/intersect.html
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bed1:
+        type: file
+        description: Bed file, each feature in 1 is compared to 2 in search of overlaps
+        pattern: "*.{bed}"
+    - bed2:
+        type: file
+        description: Second bed file, used to compare to 1.
+        pattern: "*.{bed}"
+
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bed:
+        type: file
+        description: Overlapped bed file
+        pattern: "*.{intersect.bed}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    -"@Emiller88"
+    -"@sruthipsuresh"

software/bedtools/merge/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/bedtools/merge/main.nf

@@ -0,0 +1,40 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BEDTOOLS_MERGE {
+    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:'') }
+
+    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(beds)
+
+    output:
+    tuple val(meta), path('*.merged.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 \\
+        merge \\
+        -i $beds \\
+        $options.args \\
+        > ${prefix}.merged.bed
+
+    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    """
+}

software/bedtools/merge/meta.yml

@@ -0,0 +1,55 @@
+name: bedtools_merge
+description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features.
+keywords:
+    - bed
+    - merge
+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/merge.html
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bed:
+        type: file
+        description: Presorted interval 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: Overlapped bed file with combined features
+        pattern: "*.{merged.bed}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    -"@Emiller88"
+    -"@sruthipsuresh"

software/bedtools/slop/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/bedtools/slop/main.nf

@@ -0,0 +1,43 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BEDTOOLS_SLOP {
+    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(beds), path (sizes)
+
+    output:
+    tuple val(meta), path("*.slop.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 \\
+        slop \\
+        -i $beds \\
+        -g $sizes \\
+        $options.args \\
+        > ${prefix}.slop.bed
+
+    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    """
+
+}

software/bedtools/slop/meta.yml

@@ -0,0 +1,75 @@
+name: bedtools_slop
+description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r)
+keywords:
+  - bed
+  - slopBed
+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/slop.html
+
+params:
+  - l:
+      type: integer
+      description: The number of base pairs to subtract from the start coordinate
+  - r:
+      type: integer
+      description: The number of base pairs to add to the end coordinate
+  - b:
+      type: integer
+      description: Increases the entry by the same number base pairs in each direction
+  - pct:
+      type: boolean
+      description: |
+        Define -l and -r as a fraction of the feature’s length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. By default this is set to false.
+
+  - header:
+      type: boolean
+      description: |
+        Print the header from the input file prior to results.
+
+  - outdir:
+      type: string
+      description: |
+        The pipeline's output directory. By default, the module will
+        output files into `$params.outdir/<SOFTWARE>`
+  - publish_dir_mode:
+      type: string
+      description: |
+        Value for the Nextflow `publishDir` mode parameter.
+        Available: symlink, rellink, link, copy, copyNoFollow, move.
+  - enable_conda:
+      type: boolean
+      description: |
+        Run the module with Conda using the software specified
+        via the `conda` directive
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bed:
+      type: file
+      description: List of bed files
+      pattern: "*.{bed}"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bed:
+      type: file
+      description: Edited bed file
+      pattern: "*.{slop.bed}"
+
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+
+authors: -"@Emiller88"
+  -"@sruthipsuresh"

software/bedtools/sort/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/bedtools/sort/main.nf

@@ -0,0 +1,40 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def 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), 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(beds)
+
+    output:
+    tuple val(meta), path('*.sort.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 \\
+        sort \\
+        -i $beds \\
+        $options.args \\
+        > ${prefix}.sort.bed
+
+    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    """
+}

software/bedtools/sort/meta.yml

@@ -0,0 +1,57 @@
+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
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - beds:
+        type: file
+        description: List of bed files
+        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: "*.{sort.bed}"
+
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+
+authors:
+    -"@Emiller88"
+    -"@sruthipsuresh"

tests/software/bedtools/complement/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_COMPLEMENT } from '../../../../software/bedtools/complement/main.nf' addParams( options: [:] )
+
+workflow test_bedtools_complement {
+    def input = []
+    input = [ [ id:'test'],
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
+              file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ]
+
+    BEDTOOLS_COMPLEMENT( input )
+}

tests/software/bedtools/complement/test.yml

@@ -0,0 +1,8 @@
+- name: bedtools complement
+  command: nextflow run ./tests/software/bedtools/complement -entry test_bedtools_complement -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_complement
+  files:
+    - path: output/bedtools/test.complement.bed
+      md5sum: 55a43973abb1a08ac57290ff44f6c502

tests/software/bedtools/genomecov/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_GENOMECOV } from '../../../../software/bedtools/genomecov/main.nf' addParams( options: [:] )
+
+
+workflow test_bedtools_genomecov {
+    def input = []
+    input = [ [ id:'test'],
+              file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
+
+    BEDTOOLS_GENOMECOV( input )
+}
+

tests/software/bedtools/genomecov/test.yml

@@ -0,0 +1,8 @@
+- name: bedtools genomecov
+  command: nextflow run ./tests/software/bedtools/genomecov -entry test_bedtools_genomecov -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_genomecov
+  files:
+    - path: output/bedtools/test.bed
+      md5sum: 8c8238ca3cdac7a0e650ade95ee941f4

tests/software/bedtools/intersect/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_INTERSECT } from '../../../../software/bedtools/intersect/main.nf' addParams( options: [:] )
+
+workflow test_bedtools_intersect {
+    def input = []
+    input = [ [ id:'test'],
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
+              file("${launchDir}/tests/data/bed/B.bed", checkIfExists: true) ]
+
+    BEDTOOLS_INTERSECT( input )
+}

tests/software/bedtools/intersect/test.yml

@@ -0,0 +1,8 @@
+- name: bedtools intersect
+  command: nextflow run ./tests/software/bedtools/intersect -entry test_bedtools_intersect -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_intersect
+  files:
+    - path: output/bedtools/test.intersect.bed
+      md5sum: cc1bb317886e7df0a942b56f8a320d9c

tests/software/bedtools/merge/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_MERGE } from '../../../../software/bedtools/merge/main.nf' addParams( options: [:] )
+
+workflow test_bedtools_merge {
+    def input = []
+    input = [ [ id:'test'],
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
+
+    BEDTOOLS_MERGE( input )
+}
+

tests/software/bedtools/merge/test.yml

@@ -0,0 +1,8 @@
+- name: bedtools merge
+  command: nextflow run ./tests/software/bedtools/merge -entry test_bedtools_merge -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_merge
+  files:
+    - path: output/bedtools/test.merged.bed
+      md5sum: 13e5a3b254fac35fe0da0c92cbaf1761

tests/software/bedtools/slop/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_SLOP } from '../../../../software/bedtools/slop/main.nf' addParams( options: [args: '-l 15 -r 30'] )
+
+workflow test_bedtools_slop {
+    def input = []
+    input = [ [ id:'test'],
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
+              file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ]
+
+    BEDTOOLS_SLOP( input )
+}
+

tests/software/bedtools/slop/test.yml

@@ -0,0 +1,8 @@
+- name: bedtools slop
+  command: nextflow run ./tests/software/bedtools/slop -entry test_bedtools_slop -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_slop
+  files:
+    - path: output/bedtools/test.slop.bed
+      md5sum: 5f6ecc3e3cc6cee9537a1d088b02abec

tests/software/bedtools/sort/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BEDTOOLS_SORT } from '../../../../software/bedtools/sort/main.nf' addParams( options: [:] )
+
+workflow test_bedtools_sort {
+    def input = []
+    input = [ [ id:'test'],
+              file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
+
+    BEDTOOLS_SORT( input )
+
+}

tests/software/bedtools/sort/test.yml

@@ -0,0 +1,8 @@
+- name: bedtools sort
+  command: nextflow run ./tests/software/bedtools/sort -entry test_bedtools_sort -c tests/config/nextflow.config
+  tags:
+    - bedtools
+    - bedtools_sort
+  files:
+    - path: output/bedtools/test.sort.bed
+      md5sum: 4279202e33fcce3d19f420f1b27fddee