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Add glnexus (#729)
* Add glnexus * Fix lint error * Refactor * Suggested changes Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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68
modules/glnexus/functions.nf
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68
modules/glnexus/functions.nf
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//
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// Utility functions used in nf-core DSL2 module files
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//
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//
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// Extract name of software tool from process name using $task.process
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//
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def getSoftwareName(task_process) {
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return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
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}
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//
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// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
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//
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def initOptions(Map args) {
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def Map options = [:]
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options.args = args.args ?: ''
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options.args2 = args.args2 ?: ''
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options.args3 = args.args3 ?: ''
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options.publish_by_meta = args.publish_by_meta ?: []
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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//
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// Tidy up and join elements of a list to return a path string
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//
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def getPathFromList(path_list) {
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def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
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paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
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return paths.join('/')
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}
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//
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// Function to save/publish module results
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//
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def saveFiles(Map args) {
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if (!args.filename.endsWith('.version.txt')) {
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def ioptions = initOptions(args.options)
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def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
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if (ioptions.publish_by_meta) {
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def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
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for (key in key_list) {
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if (args.meta && key instanceof String) {
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def path = key
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if (args.meta.containsKey(key)) {
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path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
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}
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path = path instanceof String ? path : ''
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path_list.add(path)
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}
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}
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}
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if (ioptions.publish_files instanceof Map) {
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for (ext in ioptions.publish_files) {
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if (args.filename.endsWith(ext.key)) {
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def ext_list = path_list.collect()
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ext_list.add(ext.value)
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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}
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49
modules/glnexus/main.nf
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49
modules/glnexus/main.nf
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process GLNEXUS {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::glnexus=1.4.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/glnexus:1.4.1--h40d77a6_0"
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} else {
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container "quay.io/biocontainers/glnexus:1.4.1--h40d77a6_0"
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}
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input:
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tuple val(meta), path(gvcfs)
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output:
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tuple val(meta), path("*.bcf"), emit: bcf
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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// Make list of GVCFs to merge
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def input = gvcfs.collect { it.toString() }
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def avail_mem = 3
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if (!task.memory) {
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log.info '[Glnexus] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
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} else {
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avail_mem = task.memory.giga
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}
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"""
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glnexus_cli \\
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--threads $task.cpus \\
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--mem-gbytes $avail_mem \\
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$options.args \\
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${input.join(' ')} \\
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> ${prefix}.bcf
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echo \$(glnexus_cli 2>&1) | head -n 1 | sed 's/^.*release //; s/ .*\$//' > ${software}.version.txt
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"""
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}
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36
modules/glnexus/meta.yml
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36
modules/glnexus/meta.yml
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name: glnexus
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description: merge gVCF files and perform joint variant calling
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keywords:
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- merge
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- gvcf
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tools:
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- glnexus:
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description: scalable gVCF merging and joint variant calling for population sequencing projects.
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homepage: https://github.com/dnanexus-rnd/GLnexus
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documentation: https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started
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tool_dev_url: None
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doi: https://doi.org/10.1101/343970
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licence: ['Apache License 2.0']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test' ]
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- gvcfs:
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type: list
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description: Input genomic vcf files
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pattern: "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}"
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output:
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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- bcf:
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type: file
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description: merged BCF file
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pattern: "*.bcf"
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authors:
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- "@ramprasadn"
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@ -422,6 +422,10 @@ gffread:
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- modules/gffread/**
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- tests/modules/gffread/**
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glnexus:
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- modules/glnexus/**
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- tests/modules/glnexus/**
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graphmap2/align:
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- modules/graphmap2/align/**
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- tests/modules/graphmap2/align/**
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13
tests/modules/glnexus/main.nf
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13
tests/modules/glnexus/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GLNEXUS } from '../../../modules/glnexus/main.nf' addParams( options: [:] )
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workflow test_glnexus {
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input = [ [ id:'test' ], // meta map
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[ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_gz'], checkIfExists: true) ]
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]
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GLNEXUS ( input )
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}
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7
tests/modules/glnexus/test.yml
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7
tests/modules/glnexus/test.yml
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- name: glnexus test_glnexus
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command: nextflow run tests/modules/glnexus -entry test_glnexus -c tests/config/nextflow.config
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tags:
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- glnexus
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files:
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- path: output/glnexus/test.bcf
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md5sum: 33ac8c9f3ff54e6a23177ba94a449173
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