add additional ucsc tools (#506)

* add additional ucsc tools

* Update software/ucsc/wigtobigwig/meta.yml

Co-authored-by: Kevin Menden <kevin.menden@live.com>

* Update the functions.nf and software name for ucsc/wigtobigwig and bigwigaverageoverbed.

Co-authored-by: Kevin Menden <kevin.menden@live.com>

software/ucsc/bigwigaverageoverbed/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"
+        }
+    }
+}

software/ucsc/bigwigaverageoverbed/main.nf

@@ -0,0 +1,38 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process UCSC_BIGWIGAVERAGEOVERBED {
+    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::ucsc-bigwigaverageoverbed=377" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/ucsc-bigwigaverageoverbed:377--h0b8a92a_2"
+    } else {
+        container "quay.io/biocontainers/ucsc-bigwigaverageoverbed:377--h0b8a92a_2"
+    }
+
+    input:
+    tuple val(meta), path(bed)
+    path bigwig
+
+    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}"
+    """
+    # there is a bug that bigWigAverageOverBed can not handle ensembl seqlevels style.
+    bigWigAverageOverBed ${options.args} $bigwig $bed ${bed.getSimpleName()}.tab
+
+    echo \$(bigWigAverageOverBed 2>&1) | sed 's/bigWigAverageOverBed v//; s/ - Compute.*\$//' > ${software}.version.txt
+    """
+}

software/ucsc/bigwigaverageoverbed/meta.yml

@@ -0,0 +1,46 @@
+name: ucsc_bigwigaverageoverbed
+description: compute average score of bigwig over bed file
+keywords:
+  - bigwig
+  - bedGraph
+tools:
+  - ucsc:
+      description: Compute average score of big wig over each bed, which may have introns.
+      homepage: None
+      documentation: None
+      tool_dev_url: None
+      doi: ""
+      licence: ['varies; see http://genome.ucsc.edu/license']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bed:
+      type: file
+      description: bed file
+      pattern: "*.{bed}"
+  - bigwig:
+      type: file
+      description: bigwig file
+      pattern: "*.{bigwig,bw}"
+
+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: tab file
+      pattern: "*.{tab}"
+
+authors:
+  - "@jianhong"

software/ucsc/wigtobigwig/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"
+        }
+    }
+}

software/ucsc/wigtobigwig/main.nf

@@ -0,0 +1,41 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process UCSC_WIGTOBIGWIG {
+    tag '$wig'
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/ucsc-wigtobigwig:377--h0b8a92a_2"
+    } else {
+        container "quay.io/biocontainers/ucsc-wigtobigwig:377--h0b8a92a_2"
+    }
+
+    input:
+    path wig
+    path chromsizes
+
+    output:
+    path "*.bw"                   , emit: bw
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+
+    """
+    wigToBigWig \\
+        $options.args \\
+        $wig \\
+        $chromsizes \\
+        ${wig.getSimpleName()}.bw
+
+    echo \$(wigToBigWig 2>&1) | sed 's/wigToBigWig v //; s/ - Convert.*\$//' > ${software}.version.txt
+    """
+}

software/ucsc/wigtobigwig/meta.yml

@@ -0,0 +1,37 @@
+name: ucsc_wigtobigwig
+description: Convert ascii format wig file to binary big wig format
+keywords:
+  - wig
+  - bigwig
+tools:
+  - ucsc:
+      description: |
+        Convert ascii format wig file (in fixedStep, variableStep
+        or bedGraph format) to binary big wig format
+      homepage: None
+      documentation: None
+      tool_dev_url: None
+      doi: ""
+      licence: ['varies; see http://genome.ucsc.edu/license']
+
+input:
+  - wig:
+      type: file
+      description: wig file
+      pattern: "*.{wig}"
+  - chromsizes:
+      type: file
+      description: chromosome sizes file
+
+output:
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - bw:
+      type: file
+      description: bigwig file
+      pattern: "*.{bw}"
+
+authors:
+  - "@jianhong"

tests/config/pytest_software.yml

@@ -659,6 +659,14 @@ ucsc/bedgraphtobigwig:
   - software/ucsc/bedgraphtobigwig/**
   - tests/software/ucsc/bedgraphtobigwig/**
 
+ucsc/bigwigaverageoverbed:
+  - software/ucsc/bigwigaverageoverbed/**
+  - tests/software/ucsc/bigwigaverageoverbed/**
+
+ucsc/wigtobigwig:
+  - software/ucsc/wigtobigwig/**
+  - tests/software/ucsc/wigtobigwig/**
+
 unicycler:
   - software/unicycler/**
   - tests/software/unicycler/**

tests/software/ucsc/bigwigaverageoverbed/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UCSC_BIGWIGAVERAGEOVERBED } from '../../../../software/ucsc/bigwigaverageoverbed/main.nf' addParams( options: [:] )
+
+workflow test_ucsc_bigwigaverageoverbed {
+    input = [ [ id: 'test' ], // meta map
+              [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true ) ]
+            ]
+    bigwig = file(params.test_data['sarscov2']['illumina']['test_bigwig'], checkIfExists: true)
+
+    UCSC_BIGWIGAVERAGEOVERBED ( input, bigwig )
+}

tests/software/ucsc/bigwigaverageoverbed/test.yml

@@ -0,0 +1,8 @@
+- name: ucsc bigwigaverageoverbed test_ucsc_bigwigaverageoverbed
+  command: nextflow run tests/software/ucsc/bigwigaverageoverbed -entry test_ucsc_bigwigaverageoverbed -c tests/config/nextflow.config
+  tags:
+    - ucsc
+    - ucsc/bigwigaverageoverbed
+  files:
+    - path: output/ucsc/test.tab
+      md5sum: d92334d90353577571eaf777933dce9b

tests/software/ucsc/wigtobigwig/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { UCSC_WIGTOBIGWIG } from '../../../../software/ucsc/wigtobigwig/main.nf' addParams( options: [:] )
+
+workflow test_ucsc_wigtobigwig {
+
+    input = file(params.test_data['sarscov2']['illumina']['test_wig_gz'], checkIfExists: true)
+
+    sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
+
+    UCSC_WIGTOBIGWIG ( input, sizes )
+}

tests/software/ucsc/wigtobigwig/test.yml

@@ -0,0 +1,8 @@
+- name: ucsc wigtobigwig test_ucsc_wigtobigwig
+  command: nextflow run tests/software/ucsc/wigtobigwig -entry test_ucsc_wigtobigwig -c tests/config/nextflow.config
+  tags:
+    - ucsc
+    - ucsc/wigtobigwig
+  files:
+    - path: output/ucsc/test.bw
+      md5sum: b64af7003665dc51fae958216b06ed95