Adding module bowtie2 align

software/bowtie2/align/functions.nf

@@ -0,0 +1,60 @@
+
+/*
+ * -----------------------------------------------------
+ *  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/bowtie2/align/main.nf

@@ -0,0 +1,72 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BOWTIE2_ALIGN {
+    tag "$meta.id"
+    label 'process_high'
+    publishDir "${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::bowtie2=2.4.2 bioconda::samtools=1.11 conda-forge::pigz=2.3.4' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0"
+    } else {
+        container "quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0"
+    }
+
+    input:
+    tuple val(meta), path(reads)
+    path  index
+
+    output:
+    tuple val(meta), path('*.bam'), emit: bam
+    tuple val(meta), path('*.log'), emit: log
+    path  '*.version.txt'         , emit: version
+    tuple val(meta), path('*fastq.gz'), optional:true, emit: fastq
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    if (meta.single_end) {
+        def unaligned = params.save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
+        """
+        INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
+        bowtie2 \\
+            -x \$INDEX \\
+            -U $reads \\
+            --threads $task.cpus \\
+            $unaligned \\
+            $options.args \\
+            2> ${prefix}.bowtie2.log \\
+            | samtools view -@ $task.cpus $options.args2 -bhS -o ${prefix}.bam -
+
+        echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
+        """
+    } else {
+        def unaligned = params.save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
+        """
+        INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
+        bowtie2 \\
+            -x \$INDEX \\
+            -1 ${reads[0]} \\
+            -2 ${reads[1]} \\
+            --threads $task.cpus \\
+            $unaligned \\
+            $options.args \\
+            2> ${prefix}.bowtie2.log \\
+            | samtools view -@ $task.cpus $options.args2 -bhS -o ${prefix}.bam -
+
+        if [ -f ${prefix}.unmapped.fastq.1.gz ]; then
+            mv ${prefix}.unmapped.fastq.1.gz ${prefix}.unmapped_1.fastq.gz
+        fi
+        if [ -f ${prefix}.unmapped.fastq.2.gz ]; then
+            mv ${prefix}.unmapped.fastq.2.gz ${prefix}.unmapped_2.fastq.gz
+        fi
+        echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
+        """
+    }
+}

software/bowtie2/build/meta.yml

@@ -7,9 +7,10 @@ keywords:
     - genome
     - reference
 tools:
-    - bowtie:
+    - bowtie2:
           description: |
-              Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.
+              Bowtie 2 is an ultrafast and memory-efficient tool for aligning
+              sequencing reads to long reference sequences.
           homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
           documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
           doi: 10.1038/nmeth.1923
@@ -49,3 +50,5 @@ output:
           pattern: "*.{version.txt}"
 authors:
     - "@kevinmenden"
+    - "@joseespinosa"
+    - "drpatelh"