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Initial commit mummer module (#940)
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78
modules/mummer/functions.nf
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78
modules/mummer/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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// Extract name of module from process name using $task.process
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//
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def getProcessName(task_process) {
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return task_process.tokenize(':')[-1]
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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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def ioptions = initOptions(args.options)
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def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
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// Do not publish versions.yml unless running from pytest workflow
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if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
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return null
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}
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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)}/$args.filename"
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}
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}
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55
modules/mummer/main.nf
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55
modules/mummer/main.nf
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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def VERSION = '3.23'
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process MUMMER {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::mummer=3.23" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12"
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} else {
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container "quay.io/biocontainers/mummer:3.23--pl5262h1b792b2_12"
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}
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input:
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tuple val(meta), path(ref), path(query)
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output:
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tuple val(meta), path("*.coords"), emit: coords
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def is_compressed_ref = ref.getName().endsWith(".gz") ? true : false
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def fasta_name_ref = ref.getName().replace(".gz", "")
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def is_compressed_query = query.getName().endsWith(".gz") ? true : false
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def fasta_name_query = query.getName().replace(".gz", "")
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"""
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if [ "$is_compressed_ref" == "true" ]; then
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gzip -c -d $ref > $fasta_name_ref
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fi
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if [ "$is_compressed_query" == "true" ]; then
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gzip -c -d $query > $fasta_name_query
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fi
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mummer \\
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$options.args \\
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$fasta_name_ref \\
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$fasta_name_query \\
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> ${prefix}.coords
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( echo $VERSION )
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END_VERSIONS
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"""
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}
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48
modules/mummer/meta.yml
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48
modules/mummer/meta.yml
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name: mummer
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description: MUMmer is a system for rapidly aligning entire genomes
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keywords:
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- align
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- genome
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- fasta
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tools:
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- mummer:
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description: MUMmer is a system for rapidly aligning entire genomes
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homepage: http://mummer.sourceforge.net/
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documentation: http://mummer.sourceforge.net/
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tool_dev_url: http://mummer.sourceforge.net/
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doi: https://doi.org/10.1186/gb-2004-5-2-r12
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licence: ['The Artistic License']
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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', single_end:false ]
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- ref:
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type: file
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description: FASTA file of the reference sequence
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pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}"
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- query:
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type: file
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description: FASTA file of the query sequence
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pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}"
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output:
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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', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- coords:
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type: file
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description: File containing coordinates of matches between reference and query sequence
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pattern: "*.coords"
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authors:
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- "@mjcipriano"
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- "@sateeshperi"
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@ -867,6 +867,10 @@ multiqc:
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- modules/multiqc/**
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- tests/modules/multiqc/**
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mummer:
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- modules/mummer/**
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- tests/modules/mummer/**
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muscle:
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- modules/muscle/**
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- tests/modules/muscle/**
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14
tests/modules/mummer/main.nf
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14
tests/modules/mummer/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { MUMMER } from '../../../modules/mummer/main.nf' addParams( options: [:] )
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workflow test_mummer {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true) ]
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MUMMER ( input )
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}
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7
tests/modules/mummer/test.yml
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7
tests/modules/mummer/test.yml
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- name: mummer test_mummer
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command: nextflow run tests/modules/mummer -entry test_mummer -c tests/config/nextflow.config
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tags:
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- mummer
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files:
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- path: output/mummer/test.coords
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md5sum: 6084fe43c7cb2eca8b96d674560bdefc
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