Add glnexus (#729)

* Add glnexus

* Fix lint error

* Refactor

* Suggested changes

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

modules/glnexus/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/glnexus/main.nf

@@ -0,0 +1,49 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options        = initOptions(params.options)
+
+process GLNEXUS {
+    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::glnexus=1.4.1" : null)
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0"
+    } else {
+        container "quay.io/biocontainers/glnexus:1.4.1--h40d77a6_0"
+    }
+
+    input:
+    tuple val(meta), path(gvcfs)
+
+    output:
+    tuple val(meta), path("*.bcf"), emit: bcf
+    path "*.version.txt"          , emit: version
+
+    script:
+    def software = getSoftwareName(task.process)
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    // Make list of GVCFs to merge
+    def input = gvcfs.collect { it.toString() }
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[Glnexus] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    glnexus_cli \\
+        --threads $task.cpus \\
+        --mem-gbytes $avail_mem \\
+        $options.args \\
+        ${input.join(' ')} \\
+        > ${prefix}.bcf
+    echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release //; s/ .*\$//' > ${software}.version.txt
+    """
+}

modules/glnexus/meta.yml

@@ -0,0 +1,36 @@
+name: glnexus
+description: merge gVCF files and perform joint variant calling
+keywords:
+  - merge
+  - gvcf
+tools:
+  - glnexus:
+      description: scalable gVCF merging and joint variant calling for population sequencing projects.
+      homepage: https://github.com/dnanexus-rnd/GLnexus
+      documentation: https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started
+      tool_dev_url: None
+      doi: https://doi.org/10.1101/343970
+      licence: ['Apache License 2.0']
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test' ]
+  - gvcfs:
+      type: list
+      description: Input genomic vcf files
+      pattern: "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}"
+
+output:
+  - version:
+      type: file
+      description: File containing software version
+      pattern: "*.{version.txt}"
+  - bcf:
+      type: file
+      description: merged BCF file
+      pattern: "*.bcf"
+authors:
+  - "@ramprasadn"

tests/config/pytest_modules.yml

@@ -422,6 +422,10 @@ gffread:
   - modules/gffread/**
   - tests/modules/gffread/**
 
+glnexus:
+  - modules/glnexus/**
+  - tests/modules/glnexus/**
+
 graphmap2/align:
   - modules/graphmap2/align/**
   - tests/modules/graphmap2/align/**

tests/modules/glnexus/main.nf

@@ -0,0 +1,13 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GLNEXUS } from '../../../modules/glnexus/main.nf' addParams( options: [:] )
+
+workflow test_glnexus {
+    input = [ [ id:'test' ], // meta map
+              [ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
+              file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz'], checkIfExists: true) ]
+            ]
+    GLNEXUS ( input )
+}

tests/modules/glnexus/test.yml

@@ -0,0 +1,7 @@
+- name: glnexus test_glnexus
+  command: nextflow run tests/modules/glnexus -entry test_glnexus -c tests/config/nextflow.config
+  tags:
+    - glnexus
+  files:
+    - path: output/glnexus/test.bcf
+      md5sum: 33ac8c9f3ff54e6a23177ba94a449173