added classic mlst module (#742)

* added classic mlst module

* removed nf-core TODO comments

* included drpatelh suggestions

* adjust version capture identation

* update main to pass lint

* follow output expected by test.yml

* suggested prefix change from rpetit3

* Apply suggestions from code review

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

modules/mlst/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+    // Do not publish versions.yml unless running from pytest workflow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/mlst/main.nf

@@ -0,0 +1,42 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process MLST {
+    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::mlst=2.19.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/mlst:2.19.0--hdfd78af_1"
+    } else {
+        container "quay.io/biocontainers/mlst:2.19.0--hdfd78af_1"
+    }
+
+    input:
+    tuple val(meta), path(fasta)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    path "versions.yml"           , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    mlst \\
+        --threads $task.cpus \\
+        $fasta \\
+        > ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( echo \$(mlst --version 2>&1) | sed 's/mlst //' )
+    END_VERSIONS
+    """
+
+}

modules/mlst/meta.yml

@@ -0,0 +1,42 @@
+name: mlst
+description: Run Torsten Seemann's classic MLST on a genome assembly
+keywords:
+  - mlst
+tools:
+  - mlst:
+      description: Scan contig files against PubMLST typing schemes
+      homepage: None
+      documentation: None
+      tool_dev_url: None
+      doi: ""
+      licence: ['GPL v2']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fasta:
+      type: file
+      description: Assembly fasta file
+      pattern: "*.{fasta,fa,fna}"
+
+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"
+  - tsv:
+      type: file
+      description: MLST calls in tsv format
+      pattern: "*.{tsv}"
+
+authors:
+  - "@lskatz"
+  - "@tseemann"

tests/config/pytest_modules.yml

@@ -634,6 +634,10 @@ minimap2/index:
   - modules/minimap2/index/**
   - tests/modules/minimap2/index/**
 
+mlst:
+  - modules/mlst/**
+  - tests/modules/mlst/**
+
 mosdepth:
   - modules/mosdepth/**
   - tests/modules/mosdepth/**

tests/modules/mlst/main.nf

@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { MLST } from '../../../modules/mlst/main.nf' addParams( options: [:] )
+
+workflow test_mlst {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              file("https://raw.githubusercontent.com/nf-core/test-datasets/bactmap/genome/NCTC13799.fna", checkIfExists: true) ]
+
+    MLST ( input )
+}

tests/modules/mlst/test.yml

@@ -0,0 +1,7 @@
+- name: mlst test_mlst
+  command: nextflow run tests/modules/mlst -entry test_mlst -c tests/config/nextflow.config
+  tags:
+    - mlst
+  files:
+    - path: output/mlst/test.tsv
+      md5sum: b52df6178834a156c9402012718eb65e