Add bedtools/makewindows module (#658)

* Add bedtools/makewindows module

modules/bedtools/makewindows/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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"
+        }
+    }
+}

modules/bedtools/makewindows/main.nf

@@ -0,0 +1,42 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process BEDTOOLS_MAKEWINDOWS {
+    tag "$meta.id"
+    label 'process_low'
+    publishDir "${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--h7d7f7ad_1"
+    } else {
+        container "quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_1"
+    }
+
+    input:
+    tuple val(meta), path(regions)
+    val(use_bed)
+
+    output:
+    tuple val(meta), path("*.tab"), emit: tab
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def arg_input = use_bed ? "-b $regions" : "-g $regions"
+    """
+    bedtools \\
+        makewindows \\
+        ${arg_input} \\
+        $options.args \\
+        > ${prefix}.tab
+
+    echo \$(bedtools --version) | sed -e "s/bedtools v//g" > ${software}.version.txt
+    """
+}

modules/bedtools/makewindows/meta.yml

@@ -0,0 +1,43 @@
+name: bedtools_makewindows
+
+description: Makes adjacent or sliding windows across a genome or BED file.
+keywords:
+  - bed
+  - windows
+tools:
+  - bedtools:
+      description: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
+      homepage: https://bedtools.readthedocs.io
+      documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html
+      tool_dev_url: None
+      doi: "10.1093/bioinformatics/btq033"
+      licence: ['GPL v2']
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - regions:
+      type: file
+      description: BED file OR Genome details file (<chromName><TAB><chromSize>)
+      pattern: "*.{bed,fai,tab}"
+  - use_bed:
+      type: boolean
+      description: true = input is a BED file; false = input is a genome details file
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - tab:
+      type: file
+      description: Windows TAB file (BED or BED-like format)
+      pattern: "*.tab"
+authors:
+  - "@kevbrick"

tests/config/pytest_modules.yml

@@ -90,6 +90,10 @@ bedtools/intersect:
   - modules/bedtools/intersect/**
   - tests/modules/bedtools/intersect/**
 
+bedtools/makewindows:
+  - modules/bedtools/makewindows/**
+  - tests/modules/bedtools/makewindows/**
+
 bedtools/maskfasta:
   - modules/bedtools/maskfasta/**
   - tests/modules/bedtools/maskfasta/**

tests/modules/bedtools/makewindows/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+test_options = ['args': '-w 50 ']
+include { BEDTOOLS_MAKEWINDOWS } from '../../../../modules/bedtools/makewindows/main.nf' addParams( options: test_options )
+
+workflow test_bedtools_makewindows {
+    
+    input = [ [ id:'test'],
+              file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
+
+    BEDTOOLS_MAKEWINDOWS ( input, true )
+}

tests/modules/bedtools/makewindows/test.yml

@@ -0,0 +1,8 @@
+- name: bedtools makewindows test_bedtools_makewindows
+  command: nextflow run tests/modules/bedtools/makewindows -entry test_bedtools_makewindows -c tests/config/nextflow.config
+  tags:
+    - bedtools/makewindows
+    - bedtools
+  files:
+    - path: output/bedtools/test.tab
+      md5sum: 0cf6ed2b6f470cd44a247da74ca4fe4e