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Implement plink/extract
module (#901)
* Implement PLINK_EXTRACT module * fix plink version number * Update main.nf * Update test_data.config * Update modules/plink/extract/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * just use one channel * fix test with new channel input Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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78
modules/plink/extract/functions.nf
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78
modules/plink/extract/functions.nf
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@ -0,0 +1,78 @@
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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)}/$args.filename"
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}
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}
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47
modules/plink/extract/main.nf
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47
modules/plink/extract/main.nf
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process PLINK_EXTRACT {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1"
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} else {
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container "quay.io/biocontainers/plink:1.90b6.21--h779adbc_1"
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}
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input:
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tuple val(meta), path(bed), path(bim), path(fam), path(variants)
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output:
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tuple val(meta), path("*.bed"), emit: bed
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tuple val(meta), path("*.bim"), emit: bim
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tuple val(meta), path("*.fam"), emit: fam
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use the suffix option to disambiguate"
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"""
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plink \\
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--bfile ${meta.id} \\
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$options.args \\
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--extract $variants \\
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--threads $task.cpus \\
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--make-bed \\
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--out $prefix
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
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END_VERSIONS
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"""
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}
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62
modules/plink/extract/meta.yml
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62
modules/plink/extract/meta.yml
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name: plink_extract
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description: Subset plink bfiles with a text file of variant identifiers
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keywords:
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- extract
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- plink
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tools:
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- plink:
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description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
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homepage: None
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documentation: None
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tool_dev_url: None
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doi: ""
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licence: ['GPL']
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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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- bed:
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type: file
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description: PLINK binary biallelic genotype table
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pattern: "*.{bed}"
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- bim:
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type: file
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description: PLINK extended MAP file
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pattern: "*.{bim}"
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- fam:
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type: file
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description: PLINK sample information file
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pattern: "*.{fam}"
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- variants:
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type: file
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description: A text file containing variant identifiers to keep (one per line)
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pattern: "*.{keep}"
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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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- bed:
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type: file
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description: PLINK binary biallelic genotype table
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pattern: "*.{bed}"
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- bim:
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type: file
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description: PLINK extended MAP file
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pattern: "*.{bim}"
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- fam:
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type: file
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description: PLINK sample information file
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pattern: "*.{fam}"
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authors:
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- "@nebfield"
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@ -936,6 +936,10 @@ plasmidid:
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- modules/plasmidid/**
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- tests/modules/plasmidid/**
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plink/extract:
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- modules/plink/extract/**
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- tests/modules/plink/extract/**
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plink/vcf:
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- modules/plink/vcf/**
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- tests/modules/plink/vcf/**
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@ -119,8 +119,10 @@ params {
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gnomad_r2_1_1_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi"
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mills_and_1000g_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
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mills_and_1000g_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
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syntheticvcf_short_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz"
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syntheticvcf_short_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
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index_salmon = "${test_data_dir}/genomics/homo_sapiens/genome/index/salmon"
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repeat_expansions = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json"
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}
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29
tests/modules/plink/extract/main.nf
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29
tests/modules/plink/extract/main.nf
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PLINK_VCF } from '../../../../modules/plink/vcf/main.nf' addParams ( options: [args:'--make-bed --set-missing-var-ids @:#:\\$1:\\$2'])
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include { PLINK_EXTRACT } from '../../../../modules/plink/extract/main.nf' addParams( options: [suffix:'.extract'] )
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workflow test_plink_extract {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
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]
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PLINK_VCF ( input )
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PLINK_VCF.out.bim
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.splitText(file: 'variants.keep', keepHeader: false, by: 10)
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.first()
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.set { ch_variants }
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PLINK_VCF.out.bed
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.concat(PLINK_VCF.out.bim, PLINK_VCF.out.fam.concat(ch_variants))
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.groupTuple()
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.map{ meta, paths -> [meta, paths[0], paths[1], paths[2], paths[3]] }
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.set { ch_extract }
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PLINK_EXTRACT ( ch_extract )
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}
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18
tests/modules/plink/extract/test.yml
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18
tests/modules/plink/extract/test.yml
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- name: plink extract test_plink_extract
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command: nextflow run tests/modules/plink/extract -entry test_plink_extract -c tests/config/nextflow.config
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tags:
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- plink
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- plink/extract
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files:
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- path: output/plink/test.bed
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md5sum: 9121010aba9905eee965e96bc983611d
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- path: output/plink/test.bim
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md5sum: 510ec606219ee5daaf5c207cb01554bf
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- path: output/plink/test.extract.bed
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md5sum: 9e02f7143bcc756a51f20d50ca7f8032
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- path: output/plink/test.extract.bim
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md5sum: 63d190aea4094aa5d042aacd63397f94
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- path: output/plink/test.extract.fam
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md5sum: c499456df4da78792ef29934ef3cd47d
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- path: output/plink/test.fam
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md5sum: c499456df4da78792ef29934ef3cd47d
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