add new iqtree module (#427)

* add new iqtree module

* Resolve suggests after PR review

* add newline to functions

software/iqtree/functions.nf

@@ -0,0 +1,70 @@
+/*
+ * -----------------------------------------------------
+ *  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"
+        }
+    }
+}

software/iqtree/main.nf

@@ -0,0 +1,44 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process IQTREE {
+    tag "$variant_alignment"
+    label 'process_medium'
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
+
+    conda (params.enable_conda ? "bioconda::iqtree=2.1.2" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/iqtree:2.1.2--h56fc30b_0"
+    } else {
+        container "quay.io/biocontainers/iqtree:2.1.2--h56fc30b_0"
+    }
+
+    input:
+    path alignment
+    val constant_sites
+
+    output:
+    path "*.treefile",    emit: phylogeny
+    path "*.version.txt", emit: version
+
+    script:
+    def software    = getSoftwareName(task.process)
+    def fconst_args = constant_sites ? '-fconst $constant_sites' : ''
+    def memory      = task.memory.toString().replaceAll(' ', '')
+    """
+    iqtree \\
+        $fconst_args \\
+        $options.args \\
+        -s $alignment \\
+        -nt AUTO \\
+        -ntmax $task.cpus \\
+        -mem $memory \\
+
+    echo \$(iqtree -version 2>&1) | sed 's/^IQ-TREE multicore version \\([0-9\\.]*\\) .*\$/\\1/' > ${software}.version.txt
+    """
+}

software/iqtree/meta.yml

@@ -0,0 +1,34 @@
+name: iqtree
+description: Produces a Newick format phylogeny from a multiple sequence alignment using the maxium likelihood algorithm. Capable of bacterial genome size alignments.
+keywords:
+  - phylogeny
+  - newick
+  - maximum likelihood
+tools:
+  - iqtree:
+      description: Efficient phylogenomic software by maximum likelihood.
+      homepage: http://www.iqtree.org
+      documentation: http://www.iqtree.org/doc
+      tool_dev_url: https://github.com/iqtree/iqtree2
+      doi: doi.org/10.1093/molbev/msaa015
+      licence: ['GPL v2-or-later']
+
+input:
+  - alignment:
+      type: file
+      description: A FASTA format multiple sequence alignment file
+      pattern: "*.{fasta,fas,fa,mfa}"
+
+output:
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - phylogeny:
+      type: file
+      description: A phylogeny in Newick format
+      pattern: "*.{treefile}"
+
+authors:
+  - "@avantonder"
+  - "@aunderwo"

tests/config/pytest_software.yml

@@ -277,6 +277,10 @@ homer/annotatepeaks:
   - software/homer/annotatepeaks/**
   - tests/software/homer/annotatepeaks/**
 
+iqtree:
+  - software/iqtree/**
+  - tests/software/iqtree/**
+
 ivar/consensus:
   - software/ivar/consensus/**
   - tests/software/ivar/consensus/**

tests/software/iqtree/main.nf

@@ -0,0 +1,12 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { IQTREE } from '../../../software/iqtree/main.nf' addParams( options: [:] )
+
+workflow test_iqtree {
+    
+    input = [ file(params.test_data['sarscov2']['genome']['informative_sites_fas'], checkIfExists: true) ]
+
+    IQTREE ( input, '' )
+}

tests/software/iqtree/test.yml

@@ -0,0 +1,11 @@
+- name: iqtree
+  command: nextflow run ./tests/software/iqtree -entry test_iqtree -c tests/config/nextflow.config
+  tags:
+    - iqtree
+  files:
+    - path: output/iqtree/informative_sites.fas.treefile
+      contains:
+        - '(sample1:0.002'
+        - '(sample2:0.005'
+        - 'sample3:0.0005'
+        - 'sample4:0.001'