Add bedtools/makewindows module (#658)

* Add bedtools/makewindows module
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Kevin Brick 2021-09-07 14:36:06 -04:00 committed by GitHub
parent 0f59b07945
commit 0732028e15
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6 changed files with 179 additions and 0 deletions

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//
// Utility functions used in nf-core DSL2 module files
//
//
// Extract name of software tool from process name using $task.process
//
def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
}
//
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
//
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.args3 = args.args3 ?: ''
options.publish_by_meta = args.publish_by_meta ?: []
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
//
// Tidy up and join elements of a list to return a path string
//
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
//
// Function to save/publish module results
//
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
if (ioptions.publish_by_meta) {
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
for (key in key_list) {
if (args.meta && key instanceof String) {
def path = key
if (args.meta.containsKey(key)) {
path = args.meta[key] instanceof Boolean ? "${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 } from './functions'
params.options = [:]
options = initOptions(params.options)
process BEDTOOLS_MAKEWINDOWS {
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::bedtools=2.30.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_1"
} else {
container "quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_1"
}
input:
tuple val(meta), path(regions)
val(use_bed)
output:
tuple val(meta), path("*.tab"), emit: tab
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def arg_input = use_bed ? "-b $regions" : "-g $regions"
"""
bedtools \\
makewindows \\
${arg_input} \\
$options.args \\
> ${prefix}.tab
echo \$(bedtools --version) | sed -e "s/bedtools v//g" > ${software}.version.txt
"""
}

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name: bedtools_makewindows
description: Makes adjacent or sliding windows across a genome or BED file.
keywords:
- bed
- windows
tools:
- bedtools:
description: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
homepage: https://bedtools.readthedocs.io
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html
tool_dev_url: None
doi: "10.1093/bioinformatics/btq033"
licence: ['GPL v2']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- regions:
type: file
description: BED file OR Genome details file (<chromName><TAB><chromSize>)
pattern: "*.{bed,fai,tab}"
- use_bed:
type: boolean
description: true = input is a BED file; false = input is a genome details file
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
- tab:
type: file
description: Windows TAB file (BED or BED-like format)
pattern: "*.tab"
authors:
- "@kevbrick"

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@ -90,6 +90,10 @@ bedtools/intersect:
- modules/bedtools/intersect/**
- tests/modules/bedtools/intersect/**
bedtools/makewindows:
- modules/bedtools/makewindows/**
- tests/modules/bedtools/makewindows/**
bedtools/maskfasta:
- modules/bedtools/maskfasta/**
- tests/modules/bedtools/maskfasta/**

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
test_options = ['args': '-w 50 ']
include { BEDTOOLS_MAKEWINDOWS } from '../../../../modules/bedtools/makewindows/main.nf' addParams( options: test_options )
workflow test_bedtools_makewindows {
input = [ [ id:'test'],
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
BEDTOOLS_MAKEWINDOWS ( input, true )
}

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- name: bedtools makewindows test_bedtools_makewindows
command: nextflow run tests/modules/bedtools/makewindows -entry test_bedtools_makewindows -c tests/config/nextflow.config
tags:
- bedtools/makewindows
- bedtools
files:
- path: output/bedtools/test.tab
md5sum: 0cf6ed2b6f470cd44a247da74ca4fe4e