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>
This commit is contained in:
Benjamin Wingfield 2021-11-09 14:03:13 +00:00 committed by GitHub
parent 6d3d8306e1
commit 6bb4a6a7ee
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7 changed files with 240 additions and 0 deletions

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@ -0,0 +1,78 @@
//
// Utility functions used in nf-core DSL2 module files
//
//
// Extract name of software tool from process name using $task.process
//
def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
}
//
// Extract name of module from process name using $task.process
//
def getProcessName(task_process) {
return task_process.tokenize(':')[-1]
}
//
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
//
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_meta = args.publish_by_meta ?: []
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
//
// Tidy up and join elements of a list to return a path string
//
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
//
// Function to save/publish module results
//
def saveFiles(Map args) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
// Do not publish versions.yml unless running from pytest workflow
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
return null
}
if (ioptions.publish_by_meta) {
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
for (key in key_list) {
if (args.meta && key instanceof String) {
def path = key
if (args.meta.containsKey(key)) {
path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
}
path = path instanceof String ? path : ''
path_list.add(path)
}
}
}
if (ioptions.publish_files instanceof Map) {
for (ext in ioptions.publish_files) {
if (args.filename.endsWith(ext.key)) {
def ext_list = path_list.collect()
ext_list.add(ext.value)
return "${getPathFromList(ext_list)}/$args.filename"
}
}
} else if (ioptions.publish_files == null) {
return "${getPathFromList(path_list)}/$args.filename"
}
}

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process PLINK_EXTRACT {
tag "$meta.id"
label 'process_low'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
conda (params.enable_conda ? "bioconda::plink=1.90b6.21" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/plink:1.90b6.21--h779adbc_1"
} else {
container "quay.io/biocontainers/plink:1.90b6.21--h779adbc_1"
}
input:
tuple val(meta), path(bed), path(bim), path(fam), path(variants)
output:
tuple val(meta), path("*.bed"), emit: bed
tuple val(meta), path("*.bim"), emit: bim
tuple val(meta), path("*.fam"), emit: fam
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
if( "$bed" == "${prefix}.bed" ) error "Input and output names are the same, use the suffix option to disambiguate"
"""
plink \\
--bfile ${meta.id} \\
$options.args \\
--extract $variants \\
--threads $task.cpus \\
--make-bed \\
--out $prefix
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(plink --version) | sed 's/^PLINK v//;s/64.*//')
END_VERSIONS
"""
}

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name: plink_extract
description: Subset plink bfiles with a text file of variant identifiers
keywords:
- extract
- plink
tools:
- plink:
description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
homepage: None
documentation: None
tool_dev_url: None
doi: ""
licence: ['GPL']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: PLINK binary biallelic genotype table
pattern: "*.{bed}"
- bim:
type: file
description: PLINK extended MAP file
pattern: "*.{bim}"
- fam:
type: file
description: PLINK sample information file
pattern: "*.{fam}"
- variants:
type: file
description: A text file containing variant identifiers to keep (one per line)
pattern: "*.{keep}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- bed:
type: file
description: PLINK binary biallelic genotype table
pattern: "*.{bed}"
- bim:
type: file
description: PLINK extended MAP file
pattern: "*.{bim}"
- fam:
type: file
description: PLINK sample information file
pattern: "*.{fam}"
authors:
- "@nebfield"

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@ -936,6 +936,10 @@ plasmidid:
- modules/plasmidid/**
- tests/modules/plasmidid/**
plink/extract:
- modules/plink/extract/**
- tests/modules/plink/extract/**
plink/vcf:
- modules/plink/vcf/**
- tests/modules/plink/vcf/**

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@ -119,8 +119,10 @@ params {
gnomad_r2_1_1_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/gnomAD.r2.1.1.vcf.gz.tbi"
mills_and_1000g_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz"
mills_and_1000g_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/mills_and_1000G.indels.vcf.gz.tbi"
syntheticvcf_short_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz"
syntheticvcf_short_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/syntheticvcf_short.vcf.gz.tbi"
index_salmon = "${test_data_dir}/genomics/homo_sapiens/genome/index/salmon"
repeat_expansions = "${test_data_dir}/genomics/homo_sapiens/genome/loci/repeat_expansions.json"
}

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@ -0,0 +1,29 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { PLINK_VCF } from '../../../../modules/plink/vcf/main.nf' addParams ( options: [args:'--make-bed --set-missing-var-ids @:#:\\$1:\\$2'])
include { PLINK_EXTRACT } from '../../../../modules/plink/extract/main.nf' addParams( options: [suffix:'.extract'] )
workflow test_plink_extract {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['homo_sapiens']['genome']['syntheticvcf_short_vcf_gz'], checkIfExists: true)
]
PLINK_VCF ( input )
PLINK_VCF.out.bim
.splitText(file: 'variants.keep', keepHeader: false, by: 10)
.first()
.set { ch_variants }
PLINK_VCF.out.bed
.concat(PLINK_VCF.out.bim, PLINK_VCF.out.fam.concat(ch_variants))
.groupTuple()
.map{ meta, paths -> [meta, paths[0], paths[1], paths[2], paths[3]] }
.set { ch_extract }
PLINK_EXTRACT ( ch_extract )
}

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@ -0,0 +1,18 @@
- name: plink extract test_plink_extract
command: nextflow run tests/modules/plink/extract -entry test_plink_extract -c tests/config/nextflow.config
tags:
- plink
- plink/extract
files:
- path: output/plink/test.bed
md5sum: 9121010aba9905eee965e96bc983611d
- path: output/plink/test.bim
md5sum: 510ec606219ee5daaf5c207cb01554bf
- path: output/plink/test.extract.bed
md5sum: 9e02f7143bcc756a51f20d50ca7f8032
- path: output/plink/test.extract.bim
md5sum: 63d190aea4094aa5d042aacd63397f94
- path: output/plink/test.extract.fam
md5sum: c499456df4da78792ef29934ef3cd47d
- path: output/plink/test.fam
md5sum: c499456df4da78792ef29934ef3cd47d