Adding bowtie2_build module

software/bowtie2/build/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/build/main.nf

@@ -0,0 +1,35 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process BOWTIE2_BUILD {
+    tag "$fasta"
+    label 'process_high'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+
+    conda (params.enable_conda ? 'bioconda::bowtie2=2.4.2' : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container 'https://depot.galaxyproject.org/singularity/bowtie2:2.4.2--py38h1c8e9b9_1'
+    } else {
+        container 'quay.io/biocontainers/bowtie2:2.4.2--py38h1c8e9b9_1'
+    }
+
+    input:
+    path fasta
+
+    output:
+    path 'bowtie2'      , emit: index
+    path '*.version.txt', emit: version
+
+    script:
+    def software  = getSoftwareName(task.process)
+    """
+    mkdir bowtie2
+    bowtie2-build $options.args --threads $task.cpus $fasta bowtie2/${fasta.baseName}
+    echo \$(bowtie2 --version 2>&1) | sed 's/^.*bowtie2-align-s version //; s/ .*\$//' > ${software}.version.txt
+    """
+}

software/bowtie2/build/meta.yml

@@ -0,0 +1,51 @@
+name: bowtie2_build
+description: Builds bowtie index for reference genome
+keywords:
+    - build
+    - index
+    - fasta
+    - genome
+    - reference
+tools:
+    - bowtie:
+          description: |
+              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
+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:
+    - fasta:
+          type: file
+          description: Input genome fasta file
+output:
+    - index:
+          type: file
+          description: Bowtie2 genome index files
+          pattern: "*.bt2"
+    - version:
+          type: file
+          description: File containing software version
+          pattern: "*.{version.txt}"
+authors:
+    - "@kevinmenden"