add roary module (#776)

* add module roary

* Update meta.yml

* Update meta.yml

* Update meta.yml

* Update meta.yml

* Update main.nf

* Update meta.yml

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

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+    // Do not publish versions.yml unless running from pytest workflow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

@@ -0,0 +1,43 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process ROARY {
+    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::roary=3.13.0" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/roary:3.13.0--pl526h516909a_0"
+    } else {
+        container "quay.io/biocontainers/roary:3.13.0--pl526h516909a_0"
+    }
+
+    input:
+    tuple val(meta), path(gff)
+
+    output:
+    tuple val(meta), path("results/*")                    , emit: results
+    tuple val(meta), path("results/*.aln"), optional: true, emit: aln
+    path "versions.yml"                                   , emit: versions
+
+    script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    """
+    roary \\
+        $options.args \\
+        -p $task.cpus \\
+        -f results/ \\
+        $gff
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$( roary --version )
+    END_VERSIONS
+    """
+}

modules/roary/meta.yml

@@ -0,0 +1,47 @@
+name: roary
+description: Calculate pan-genome from annotated bacterial assemblies in GFF3 format
+keywords:
+  - gff
+  - pan-genome
+  - alignment
+tools:
+  - roary:
+      description: Rapid large-scale prokaryote pan genome analysis
+      homepage: http://sanger-pathogens.github.io/Roary/
+      documentation: http://sanger-pathogens.github.io/Roary/
+      tool_dev_url: https://github.com/sanger-pathogens/Roary/
+      doi: "http://dx.doi.org/10.1093/bioinformatics/btv421"
+      licence: ['GPL v3']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - gff:
+      type: file
+      description: A set of GFF3 formatted files
+      pattern: "*.{gff}"
+
+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"
+  - results:
+      type: directory
+      description: Directory containing Roary result files
+      pattern: "*/*"
+  - aln:
+      type: file
+      description: Core-genome alignment produced by Roary (Optional)
+      pattern: "*.{aln}"
+
+authors:
+  - "@rpetit3"

tests/config/pytest_modules.yml

@@ -811,6 +811,10 @@ raxmlng:
   - modules/raxmlng/**
   - tests/modules/raxmlng/**
 
+roary:
+  - modules/roary/**
+  - tests/modules/roary/**
+
 rsem/calculateexpression:
   - modules/rsem/calculateexpression/**
   - tests/modules/rsem/calculateexpression/**

tests/modules/roary/main.nf

@@ -0,0 +1,16 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { ROARY } from '../../../modules/roary/main.nf' addParams( options: [:] )
+
+workflow test_roary {
+    
+    input = [ [ id:'test', single_end:false ], // meta map
+              [ file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_000292685.gff", checkIfExists: true),
+                file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_000298385.gff", checkIfExists: true),
+                file("https://github.com/bactopia/bactopia-tests/raw/main/data/reference/gff/GCF_002849995.gff", checkIfExists: true) ]
+    ]
+
+    ROARY ( input )
+}

tests/modules/roary/test.yml

@@ -0,0 +1,39 @@
+- name: roary test_roary
+  command: nextflow run tests/modules/roary -entry test_roary -c tests/config/nextflow.config
+  tags:
+    - roary
+  files:
+    - path: output/roary/results/accessory.header.embl
+      contains: ['ID   Genome standard; DNA; PRO; 1234 BP.']
+    - path: output/roary/results/accessory.tab
+      contains: ['FT']
+    - path: output/roary/results/accessory_binary_genes.fa
+      md5sum: 0baeea4947bf17a2bf29d43a44f0278f
+    - path: output/roary/results/accessory_binary_genes.fa.newick
+      md5sum: b1f8c76ab231bd38b850c1f8d3c1584b
+    - path: output/roary/results/accessory_graph.dot
+      contains: ['/* list of nodes */']
+    - path: output/roary/results/blast_identity_frequency.Rtab
+      md5sum: 829baa25c3fad94b1af207265452a692
+    - path: output/roary/results/clustered_proteins
+      contains: ['JKHLNHAL_00087']
+    - path: output/roary/results/core_accessory.header.embl
+      contains: ['ID   Genome standard; DNA; PRO; 1234 BP.']
+    - path: output/roary/results/core_accessory.tab
+      contains: ['FT                   /taxa="GCF_000292685 GCF_000298385 GCF_002849995"']
+    - path: output/roary/results/core_accessory_graph.dot
+      contains: ['/* list of nodes */']
+    - path: output/roary/results/gene_presence_absence.Rtab
+      contains: ['Gene']
+    - path: output/roary/results/gene_presence_absence.csv
+      contains: ['"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences"']
+    - path: output/roary/results/number_of_conserved_genes.Rtab
+      contains: ['279']
+    - path: output/roary/results/number_of_genes_in_pan_genome.Rtab
+      contains: ['279']
+    - path: output/roary/results/number_of_new_genes.Rtab
+      contains: ['279']
+    - path: output/roary/results/number_of_unique_genes.Rtab
+      contains: ['279']
+    - path: output/roary/results/summary_statistics.txt
+      md5sum: 3921b5445df6a7ed59408119b8860a58