mirror of
https://github.com/MillironX/nf-core_modules.git
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Merge freebayes subtools (#1015)
* feat: merge freebayes subtools * fix: typo * assess comments from review * fix: path to module
This commit is contained in:
parent
4619d012e5
commit
9767b081b9
13 changed files with 148 additions and 361 deletions
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@ -4,7 +4,7 @@ include { initOptions; saveFiles; getProcessName; getSoftwareName } from './func
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params.options = [:]
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options = initOptions(params.options)
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process FREEBAYES_GERMLINE {
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process FREEBAYES {
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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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@ -19,7 +19,7 @@ process FREEBAYES_GERMLINE {
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}
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input:
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tuple val(meta), path(input), path(input_index)
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tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index)
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path fasta
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path fai
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path targets
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@ -33,6 +33,7 @@ process FREEBAYES_GERMLINE {
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def input = input_2 ? "${input_1} ${input_2}" : "${input_1}"
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def targets_file = targets ? "--target ${targets}" : ""
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def samples_file = samples ? "--samples ${samples}" : ""
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def populations_file = populations ? "--populations ${populations}" : ""
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@ -48,7 +49,7 @@ process FREEBAYES_GERMLINE {
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$populations_file \\
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$cnv_file \\
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$options.args \\
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$input > ${prefix}.vcf
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$input > ${prefix}.vcf
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gzip --no-name ${prefix}.vcf
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@ -1,11 +1,14 @@
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name: freebayes_germline
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name: freebayes
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description: A haplotype-based variant detector
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keywords:
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- variant caller
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- SNP
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- genotyping
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- variant calling
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- somatic variant calling
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- germline variant calling
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- bacterial variant calling
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- bayesian
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tools:
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- freebayes:
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description: Bayesian haplotype-based polymorphism discovery and genotyping
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@ -73,6 +76,8 @@ output:
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type: file
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description: Compressed VCF file
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pattern: "*.vcf.gz"
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authors:
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- "@maxibor"
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- "@FriederikeHanssen"
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- "@maxulysse"
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@ -1,78 +0,0 @@
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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)}/$args.filename"
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}
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}
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@ -1,74 +0,0 @@
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// Import generic module functions
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include { initOptions; saveFiles; getProcessName; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process FREEBAYES_SOMATIC {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::freebayes=1.3.5" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/freebayes:1.3.5--py38ha193a2f_3"
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} else {
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container "quay.io/biocontainers/freebayes:1.3.5--py38ha193a2f_3"
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}
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input:
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tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor)
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path fasta
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path fai
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path targets
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path samples
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output:
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tuple val(meta), path("*.vcf.gz") , emit: vcf
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def targets_file = targets ? "--target ${targets}" : ""
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def samples_file = samples ? "--samples ${samples}" : ""
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if (task.cpus > 1) {
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"""
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freebayes-parallel \\
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<(fasta_generate_regions.py ${fasta}.fai 10000) ${task.cpus} \\
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-f $fasta \\
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$targets_file \\
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$samples_file \\
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$options.args \\
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$input_tumor \\
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$input_normal > ${prefix}.vcf
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gzip --no-name ${prefix}.vcf
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(freebayes --version 2>&1) | sed 's/version:\s*v//g' )
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END_VERSIONS
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"""
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} else {
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"""
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freebayes \\
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-f $fasta \\
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$targets_file \\
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$samples_file \\
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$options.args \\
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$input_tumor \\
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$input_normal > ${prefix}.vcf
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gzip --no-name ${prefix}.vcf
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(freebayes --version 2>&1) | sed 's/version:\s*v//g' )
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END_VERSIONS
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"""
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}
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}
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@ -1,66 +0,0 @@
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name: freebayes_somatic
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description: A haplotype-based variant detector
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keywords:
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- variant caller
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- SNP
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- genotyping
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- somatic variant calling
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- bayesian
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tools:
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- freebayes:
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description: Bayesian haplotype-based polymorphism discovery and genotyping
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homepage: https://github.com/freebayes/freebayes
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documentation: https://github.com/freebayes/freebayes
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tool_dev_url: https://github.com/freebayes/freebayes
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doi: "arXiv:1207.3907"
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licence: ['MIT']
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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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- input:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- input_index:
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type: file
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description: BAM/CRAM/SAM index file
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pattern: "*.bam.bai"
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- fasta:
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type: file
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description: reference fasta file
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pattern: ".{fa,fa.gz,fasta,fasta.gz}"
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- fai:
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type: file
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description: reference fasta file index
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pattern: "*.fai"
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- targets:
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type: file
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description: Optional - Limit analysis to targets listed in this BED-format FILE.
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pattern: "*.bed"
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- samples:
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type: file
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description: Optional - Limit analysis to samples listed (one per line) in the FILE.
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pattern: "*.txt"
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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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- 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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- vcf:
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type: file
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description: Compressed VCF file
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pattern: "*.vcf.gz"
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authors:
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- "@FriederikeHanssen"
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@ -410,13 +410,9 @@ flash:
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- modules/flash/**
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- tests/modules/flash/**
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freebayes/germline:
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- modules/freebayes/germline/**
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- tests/modules/freebayes/germline/**
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freebayes/somatic:
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- modules/freebayes/somatic/**
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- tests/modules/freebayes/somatic/**
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freebayes:
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- modules/freebayes/**
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- tests/modules/freebayes/**
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gatk4/applybqsr:
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- modules/gatk4/applybqsr/**
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@ -1,51 +0,0 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FREEBAYES_GERMLINE } from '../../../../modules/freebayes/germline/main.nf' addParams( options: [:] )
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workflow test_freebayes {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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targets = []
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samples = []
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populations = []
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cnv = []
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FREEBAYES_GERMLINE ( input, fasta, fai, targets, samples, populations, cnv)
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}
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workflow test_freebayes_bed {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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targets = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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samples = []
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populations = []
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cnv = []
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FREEBAYES_GERMLINE ( input, fasta, fai, targets, samples, populations, cnv)
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}
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workflow test_freebayes_cram {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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targets = []
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samples = []
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populations = []
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cnv = []
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FREEBAYES_GERMLINE ( input, fasta, fai, targets, samples, populations, cnv)
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}
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@ -1,26 +0,0 @@
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- name: freebayes germline test_freebayes
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command: nextflow run tests/modules/freebayes/germline -entry test_freebayes -c tests/config/nextflow.config
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tags:
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- freebayes
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- freebayes/germline
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files:
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- path: output/freebayes/test.vcf.gz
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md5sum: 1ec210ad27514c7a4140c924dc66d979
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- name: freebayes germline test_freebayes_bed
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command: nextflow run tests/modules/freebayes/germline -entry test_freebayes_bed -c tests/config/nextflow.config
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tags:
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- freebayes
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- freebayes/germline
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files:
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- path: output/freebayes/test.vcf.gz
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md5sum: e8923cccd5dac196f72d3d3997a60706
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- name: freebayes germline test_freebayes_cram
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command: nextflow run tests/modules/freebayes/germline -entry test_freebayes_cram -c tests/config/nextflow.config
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tags:
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- freebayes
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- freebayes/germline
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files:
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- path: output/freebayes/test.vcf.gz
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md5sum: cb57a3ed154618e3aa4a5272fcfb7521
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95
tests/modules/freebayes/main.nf
Normal file
95
tests/modules/freebayes/main.nf
Normal file
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@ -0,0 +1,95 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FREEBAYES } from '../../../modules/freebayes/main.nf' addParams( options: [:] )
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workflow test_freebayes {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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[],
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[]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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targets = []
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samples = []
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populations = []
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cnv = []
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FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
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}
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workflow test_freebayes_bed {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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[],
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[]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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targets = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
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samples = []
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populations = []
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cnv = []
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FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
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}
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workflow test_freebayes_cram {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
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[],
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[]
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
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targets = []
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samples = []
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populations = []
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cnv = []
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FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
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}
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workflow test_freebayes_somatic {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
|
||||
]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
targets = []
|
||||
samples = []
|
||||
populations = []
|
||||
cnv = []
|
||||
|
||||
FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
|
||||
}
|
||||
|
||||
workflow test_freebayes_somatic_cram_intervals {
|
||||
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true)
|
||||
]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
targets = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||
samples = []
|
||||
populations = []
|
||||
cnv = []
|
||||
|
||||
FREEBAYES (input, fasta, fai, targets, samples, populations, cnv)
|
||||
}
|
|
@ -1,37 +0,0 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { FREEBAYES_SOMATIC } from '../../../../modules/freebayes/somatic/main.nf' addParams( options: [:] )
|
||||
|
||||
workflow test_freebayes {
|
||||
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true)
|
||||
]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
targets = []
|
||||
samples = []
|
||||
|
||||
FREEBAYES_SOMATIC ( input, fasta, fai, targets, samples)
|
||||
}
|
||||
|
||||
workflow test_freebayes_intervals {
|
||||
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true),
|
||||
file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true)
|
||||
]
|
||||
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||||
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||||
targets = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
|
||||
samples = []
|
||||
|
||||
FREEBAYES_SOMATIC ( input, fasta, fai, targets, samples)
|
||||
}
|
|
@ -1,17 +0,0 @@
|
|||
- name: freebayes somatic test_freebayes
|
||||
command: nextflow run tests/modules/freebayes/somatic -entry test_freebayes -c tests/config/nextflow.config
|
||||
tags:
|
||||
- freebayes/somatic
|
||||
- freebayes
|
||||
files:
|
||||
- path: output/freebayes/test.vcf.gz
|
||||
md5sum: 1c47d02f27ec5918558c8688ce6e7780
|
||||
|
||||
- name: freebayes somatic test_freebayes_intervals
|
||||
command: nextflow run tests/modules/freebayes/somatic -entry test_freebayes_intervals -c tests/config/nextflow.config
|
||||
tags:
|
||||
- freebayes/somatic
|
||||
- freebayes
|
||||
files:
|
||||
- path: output/freebayes/test.vcf.gz
|
||||
md5sum: 5b8a12666bde63746dcec7afcd3ef789
|
39
tests/modules/freebayes/test.yml
Normal file
39
tests/modules/freebayes/test.yml
Normal file
|
@ -0,0 +1,39 @@
|
|||
- name: freebayes test_freebayes
|
||||
command: nextflow run tests/modules/freebayes -entry test_freebayes -c tests/config/nextflow.config
|
||||
tags:
|
||||
- freebayes
|
||||
files:
|
||||
- path: output/freebayes/test.vcf.gz
|
||||
md5sum: 04d60a7135768777e0c764daec6519db
|
||||
|
||||
- name: freebayes test_freebayes_bed
|
||||
command: nextflow run tests/modules/freebayes -entry test_freebayes_bed -c tests/config/nextflow.config
|
||||
tags:
|
||||
- freebayes
|
||||
files:
|
||||
- path: output/freebayes/test.vcf.gz
|
||||
md5sum: fc6e228c8ac5508bd83da45eafc2e7b2
|
||||
|
||||
- name: freebayes test_freebayes_cram
|
||||
command: nextflow run tests/modules/freebayes -entry test_freebayes_cram -c tests/config/nextflow.config
|
||||
tags:
|
||||
- freebayes
|
||||
files:
|
||||
- path: output/freebayes/test.vcf.gz
|
||||
md5sum: 91b8caaa0e396e1ba4f264a83bb67254
|
||||
|
||||
- name: freebayes test_freebayes_somatic
|
||||
command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic -c tests/config/nextflow.config
|
||||
tags:
|
||||
- freebayes
|
||||
files:
|
||||
- path: output/freebayes/test.vcf.gz
|
||||
md5sum: 40da977199f16d9888e0e0e07e8bebee
|
||||
|
||||
- name: freebayes test_freebayes_somatic_cram_intervals
|
||||
command: nextflow run tests/modules/freebayes -entry test_freebayes_somatic_cram_intervals -c tests/config/nextflow.config
|
||||
tags:
|
||||
- freebayes
|
||||
files:
|
||||
- path: output/freebayes/test.vcf.gz
|
||||
md5sum: dd976880365287d9ad31a606eb4d091f
|
Loading…
Reference in a new issue