Add module kleborate (#711)

* initial commit [ci skip]

* remove todo from the module files [ci skip]

* add a sample test case [ci skip]

* push the latest work [ci skip]

* bump kleborate build

* test passing with the new build for kleborate [ci skip]

* ready for review

* Apply suggestions from code review

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

modules/kleborate/functions.nf

@@ -0,0 +1,68 @@
+//
+//  Utility functions used in nf-core DSL2 module files
+//
+
+//
+// Extract name of software tool from process name using $task.process
+//
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+//
+// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+//
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args            = args.args ?: ''
+    options.args2           = args.args2 ?: ''
+    options.args3           = args.args3 ?: ''
+    options.publish_by_meta = args.publish_by_meta ?: []
+    options.publish_dir     = args.publish_dir ?: ''
+    options.publish_files   = args.publish_files
+    options.suffix          = args.suffix ?: ''
+    return options
+}
+
+//
+// Tidy up and join elements of a list to return a path string
+//
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries
+    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+//
+// Function to save/publish module results
+//
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions  = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_meta) {
+            def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
+            for (key in key_list) {
+                if (args.meta && key instanceof String) {
+                    def path = key
+                    if (args.meta.containsKey(key)) {
+                        path = args.meta[key] instanceof Boolean ? "${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/kleborate/main.nf

@@ -0,0 +1,39 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process KLEBORATE {
+    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), meta:meta, publish_by_meta:['id']) }
+
+    conda (params.enable_conda ? "bioconda::kleborate=2.1.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/kleborate:2.1.0--pyhdfd78af_1"
+    } else {
+        container "quay.io/biocontainers/kleborate:2.1.0--pyhdfd78af_1"
+    }
+
+    input:
+    tuple val(meta), path(fastas)
+
+    output:
+    tuple val(meta), path("*.txt"), emit: txt
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    kleborate \\
+        $options.args \\
+        --outfile ${prefix}.results.txt \\
+        --assemblies *.fasta
+
+    echo \$(kleborate -v 2>&1) | sed 's/kleborate //;' > ${software}.version.txt
+    """
+}

modules/kleborate/meta.yml

@@ -0,0 +1,43 @@
+name: kleborate
+description: Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC).
+keywords:
+  - screening assemblies
+  - Klebsiella pneumoniae
+tools:
+  - kleborate:
+      description: Screening Klebsiella genome assemblies for MLST, sub-species, and other Klebsiella related genes of interest
+      homepage: https://github.com/katholt/Kleborate
+      documentation: https://github.com/katholt/Kleborate/wiki
+      tool_dev_url: https://github.com/katholt/Kleborate
+      doi: 10.1038/s41467-021-24448-3
+      licence: ['GPL v3 or later (GPL v3+)']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - fastas:
+      type: files
+      description: Klebsiella genome assemblies to be screened
+      pattern: "*.fasta"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - txt:
+      type: file
+      description: Result file generated after screening
+      pattern: "*.txt"
+
+authors:
+  - "@abhi18av"
+  - "@rpetit3"

tests/config/pytest_modules.yml

@@ -505,6 +505,10 @@ kallistobustools/ref:
   - modules/kallistobustools/ref/**
   - tests/modules/kallistobustools/ref/**
 
+kleborate:
+  - modules/kleborate/**
+  - tests/modules/kleborate/**
+
 kraken2/kraken2:
   - modules/kraken2/kraken2/**
   - modules/untar/**

tests/modules/kleborate/main.nf

@@ -0,0 +1,18 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { KLEBORATE } from '../../../modules/kleborate/main.nf' addParams( options: [:] )
+
+workflow test_kleborate {
+    
+    input = [ 
+        [ id:'test', single_end:false ], // meta map
+        [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
+          file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true),
+          file(params.test_data['sarscov2']['illumina']['scaffolds_fasta'], checkIfExists: true)
+        ]
+    ]
+
+    KLEBORATE ( input )
+}

tests/modules/kleborate/test.yml

@@ -0,0 +1,7 @@
+- name: kleborate
+  command: nextflow run ./tests/modules/kleborate -entry test_kleborate -c tests/config/nextflow.config
+  tags:
+    - kleborate
+  files:
+    - path: output/kleborate/test.results.txt
+      md5sum: b7979a71170736098fb8403cd92748f5