Merge pull request #171 from JoseEspinosa/mosdepth

Add mosdepth module

.github/filters.yml

@@ -148,6 +148,10 @@ minimap2_align:
   - software/minimap2/align/**
   - tests/software/minimap2/align/**
 
+mosdepth:
+  - software/mosdepth/**
+  - tests/software/mosdepth/**
+
 multiqc:
   - software/fastqc/**
   - software/multiqc/**

software/mosdepth/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/mosdepth/main.nf

@@ -0,0 +1,48 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process MOSDEPTH {
+    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::mosdepth=0.3.1' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mosdepth:0.3.1--ha7ba039_0"
+    } else {
+        container "quay.io/biocontainers/mosdepth:0.3.1--ha7ba039_0"
+    }
+
+    input:
+    tuple val(meta), path(bam), path(bai)
+    path  bed
+    val   window_size
+
+    output:
+    tuple val(meta), path('*.global.dist.txt')    , emit: global_txt
+    tuple val(meta), path('*.region.dist.txt')    , emit: regions_txt
+    tuple val(meta), path('*.summary.txt')        , emit: summary_txt
+    tuple val(meta), path('*.per-base.bed.gz')    , emit: per_base_bed
+    tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi
+    tuple val(meta), path('*.regions.bed.gz')     , emit: regions_bed
+    tuple val(meta), path('*.regions.bed.gz.csi') , emit: regions_csi
+    path  '*.version.txt'                         , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def interval = window_size ? "--by ${window_size}" : "--by ${bed}"
+    """
+    mosdepth \\
+        $interval \\
+        $options.args \\
+        $prefix \\
+        $bam
+    echo \$(mosdepth --version 2>&1) | sed 's/^.*mosdepth //; s/ .*\$//' > ${software}.version.txt
+    """
+}

software/mosdepth/meta.yml

@@ -0,0 +1,97 @@
+name: mosdepth
+description: Calculates genome-wide sequencing coverage.
+keywords:
+  - mosdepth
+  - bam
+  - cram
+  - coverage
+tools:
+  - mosdepth:
+      description: |
+        Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing.
+      documentation: https://github.com/brentp/mosdepth
+      doi: 10.1093/bioinformatics/btx699
+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
+  - singularity_pull_docker_container:
+      type: boolean
+      description: |
+        Instead of directly downloading Singularity images for use with Singularity,
+        force the workflow to pull and convert Docker containers instead.
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - bam:
+      type: file
+      description: Input BAM/CRAM file
+      pattern: "*.{bam,cram}"
+  - bai:
+      type: file
+      description: Index for BAM/CRAM file
+      pattern: "*.{bai,crai}"
+  - bed:
+      type: file
+      description: BED file with intersected intervals
+      pattern: "*.{bed}"
+  - window_size:
+      type: integer
+      description: Window size
+      pattern: "[0-9]+"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - global_txt:
+      type: file
+      description: Text file with global cumulative coverage distribution
+      pattern: "*.{global.dist.txt}"
+  - regions_txt:
+      type: file
+      description: Text file with region cumulative coverage distribution
+      pattern: "*.{region.dist.txt}"
+  - summary_txt:
+      type: file
+      description: Text file with summary mean depths per chromosome and regions
+      pattern: "*.{summary.txt}"
+  - per_base_bed:
+      type: file
+      description: BED file with per-base coverage
+      pattern: "*.{per-base.bed.gz}"
+  - per_base_csi:
+      type: file
+      description: Index file for BED file with per-base coverage
+      pattern: "*.{per-base.bed.gz.csi}"
+  - regions_bed:
+      type: file
+      description: BED file with per-region coverage
+      pattern: "*.{regions.bed.gz}"
+  - regions_csi:
+      type: file
+      description: Index file for BED file with per-region coverage
+      pattern: "*.{regions.bed.gz.csi}"
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+authors:
+    - "@joseespinosa"
+    - "@drpatelh"

tests/software/mosdepth/main.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MOSDEPTH } from '../../../software/mosdepth/main.nf' addParams( options: [:] )
+
+workflow test_mosdepth {
+
+    input = [ [ id:'test', single_end:true ],
+              [ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ],
+              [ file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam.bai", checkIfExists: true) ] ]
+    dummy = [ file("${launchDir}/tests/data/dummy/dummy_file.txt", checkIfExists: true) ]
+
+    window_size = 100
+
+    MOSDEPTH ( input, dummy, window_size )
+}

tests/software/mosdepth/test.yml

@@ -0,0 +1,19 @@
+- name: mosdepth
+  command: nextflow run ./tests/software/mosdepth -entry test_mosdepth -c tests/config/nextflow.config
+  tags:
+    - mosdepth
+  files:
+    - path: output/mosdepth/test.per-base.bed.gz
+      md5sum: 4965936f5a7502cff93286c0324e41ff
+    - path: output/mosdepth/test.regions.bed.gz
+      md5sum: 6997da219218fa57484572c3a2963dd6
+    - path: output/mosdepth/test.per-base.bed.gz.csi
+      md5sum: feed5da1defda07b6eaebcf497581115
+    - path: output/mosdepth/test.mosdepth.region.dist.txt
+      md5sum: f1f89c14bab380f44e95b09f676d0c52
+    - path: output/mosdepth/test.mosdepth.global.dist.txt
+      md5sum: 239d156c9008dc59c7f0138f6b0ba300
+    - path: output/mosdepth/test.regions.bed.gz.csi
+      md5sum:  a1c982f3e2a97f529ad5780d32010c32
+    - path: output/mosdepth/test.mosdepth.summary.txt
+      md5sum: 5a92dee6e87136a65c7973260f229852