readcounter module for hmmcopy (#1001)

* readcounter module for hmmcopy

* Changed version number

* Fix indentation

* Update main.nf

* Update modules/hmmcopy/readcounter/main.nf

Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>

Co-authored-by: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Co-authored-by: Chris Cheshire <chris.j.cheshire@gmail.com>

modules/hmmcopy/readcounter/functions.nf

@@ -0,0 +1,78 @@
+//
+//  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+    // Do not publish versions.yml unless running from pytest workflow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"
+    }
+}

modules/hmmcopy/readcounter/main.nf

@@ -0,0 +1,42 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+def VERSION = '0.1.1'
+
+process HMMCOPY_READCOUNTER {
+    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::hmmcopy=0.1.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_5"
+    } else {
+        container "quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_5"
+    }
+
+    input:
+        tuple val(meta), path(bam), path(bai)
+
+    output:
+        tuple val(meta), path("*.wig"), emit: wig
+        path "versions.yml"           , emit: versions
+
+    script:
+        def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    readCounter \\
+        $options.args \\
+        ${bam} > ${prefix}.wig
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(echo $VERSION)
+    END_VERSIONS
+    """
+}

modules/hmmcopy/readcounter/meta.yml

@@ -0,0 +1,43 @@
+name: hmmcopy_readcounter
+description: readCounter function from HMMcopy utilities, used to generate read in windows
+keywords:
+  - hmmcopy
+  - readcounter
+  - cnv
+tools:
+  - hmmcopy:
+      description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy
+      homepage: https://github.com/shahcompbio/hmmcopy_utils
+      documentation: https://github.com/shahcompbio/hmmcopy_utils
+      tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils
+      doi: ""
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - wig:
+      type: file
+      description: A wig file with the number of reads lying within each window in each chromosome
+      pattern: "*.wig"
+
+authors:
+  - "@sppearce"

tests/config/pytest_modules.yml

@@ -581,6 +581,10 @@ hmmcopy/gccounter:
   - modules/hmmcopy/gccounter/**
   - tests/modules/hmmcopy/gccounter/**
 
+hmmcopy/readcounter:
+  - modules/hmmcopy/readcounter/**
+  - tests/modules/hmmcopy/readcounter/**
+
 hmmer/hmmalign:
   - modules/hmmer/hmmalign/**
   - tests/modules/hmmer/hmmalign/**

tests/modules/hmmcopy/readcounter/main.nf

@@ -0,0 +1,14 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { HMMCOPY_READCOUNTER } from '../../../../modules/hmmcopy/readcounter/main.nf' addParams( options: [:] )
+
+workflow test_hmmcopy_readcounter {
+
+    input = [ [ id:'test'], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
+              [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)]
+            ]
+    HMMCOPY_READCOUNTER ( input )
+}

tests/modules/hmmcopy/readcounter/test.yml

@@ -0,0 +1,8 @@
+- name: hmmcopy readcounter test_hmmcopy_readcounter
+  command: nextflow run tests/modules/hmmcopy/readcounter -entry test_hmmcopy_readcounter -c tests/config/nextflow.config
+  tags:
+    - hmmcopy
+    - hmmcopy/readcounter
+  files:
+    - path: output/hmmcopy/test.wig
+      md5sum: 3655d8325baea81b3b690791262c6b57