Add module: dedup (#907)

* Specify more guidelines on input channels

* Linting

* Updates based on code review

* Update README.md

* Fix broken sentence

* feat: add megahit module, currently decompressed output

* Update main.nf

* Update tests/modules/megahit/test.yml

Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* feat: compress all outputs, remove md5sums due to gz stochasicity

* fix: wrong conda channel for pigz

* fix: broken singleend tests and update meta.yml

* Missed one

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* fix: pigz formatting

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review

* Add dedup (tests and version not working)

* Fix dedup and tests

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com>

modules/dedup/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/dedup/main.nf

@@ -0,0 +1,47 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process DEDUP {
+    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::dedup=0.12.8" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/dedup:0.12.8--hdfd78af_1"
+    } else {
+        container "quay.io/biocontainers/dedup:0.12.8--hdfd78af_1"
+    }
+
+    input:
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*_rmdup.bam"), emit: bam     // _rmdup is hardcoded output from dedup
+    tuple val(meta), path("*.json")     , emit: json
+    tuple val(meta), path("*.hist")     , emit: hist
+    tuple val(meta), path("*log")       , emit: log
+    path "versions.yml"                 , emit: versions
+
+    script:
+    prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    """
+    dedup \\
+        -Xmx${task.memory.toGiga()}g  \\
+        -i $bam \\
+        -o . \\
+        $options.args
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( echo \$(dedup --version 2>&1) | tail -n 1 | sed 's/.* v//')
+
+    END_VERSIONS
+    """
+}

modules/dedup/meta.yml

@@ -0,0 +1,60 @@
+name: dedup
+description: DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).
+keywords:
+  - dedup
+  - deduplication
+  - pcr duplicates
+  - ancient DNA
+  - paired-end
+  - bam
+tools:
+  - dedup:
+      description: DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments).
+      homepage: https://github.com/apeltzer/DeDup
+      documentation: https://dedup.readthedocs.io/en/latest/
+      tool_dev_url: https://github.com/apeltzer/DeDup
+      doi: "10.1186/s13059-016-0918-z"
+      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/SAM file
+      pattern: "*.{bam,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"
+  - bam:
+      type: file
+      description: Deduplicated BAM file
+      pattern: "*_rmdup.bam"
+  - json:
+      type: file
+      description: JSON file for MultiQC
+      pattern: "*.json"
+  - hist:
+      type: file
+      description: Histogram data of amount of deduplication
+      pattern: "*.hist"
+  - log:
+      type: file
+      description: Dedup log information
+      pattern: "*log"
+
+
+
+authors:
+  - "@jfy133"

tests/config/pytest_modules.yml

@@ -294,6 +294,10 @@ damageprofiler:
   - modules/damageprofiler/**
   - tests/modules/damageprofiler/**
 
+dedup:
+  - modules/dedup/**
+  - tests/modules/dedup/**
+
 deeptools/computematrix:
   - modules/deeptools/computematrix/**
   - tests/modules/deeptools/computematrix/**

tests/modules/dedup/main.nf

@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { DEDUP } from '../../../modules/dedup/main.nf' addParams( options: [args: "-m"] )
+
+workflow test_dedup {
+
+    input = [ [ id:'test', single_end:false ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
+
+    DEDUP ( input )
+}

tests/modules/dedup/test.yml

@@ -0,0 +1,13 @@
+- name: dedup test_dedup
+  command: nextflow run tests/modules/dedup -entry test_dedup -c tests/config/nextflow.config
+  tags:
+    - dedup
+  files:
+    - path: output/dedup/test.paired_end.dedup.json
+      md5sum: 2def0b54aba1fafa21b274f260de1b6f
+    - path: output/dedup/test.paired_end.hist
+      md5sum: df3492273a1db0d8152e35d9d5e38aa6
+    - path: output/dedup/test.paired_end.log
+      md5sum: 4b8855bd63b2f4b37da4cfb17e61fb00
+    - path: output/dedup/test.paired_end_rmdup.bam
+      md5sum: 8b0408fe3e258989095303a47e5b5061