Merge pull request #153 from JoseEspinosa/bedtools_maskfasta

Add bedtools maskfasta module
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Harshil Patel 2021-02-08 23:11:00 +00:00 committed by GitHub
commit 84cf5ea2ef
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7 changed files with 191 additions and 0 deletions

4
.github/filters.yml vendored
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@ -38,6 +38,10 @@ bedtools_intersect:
- software/bedtools/intersect/** - software/bedtools/intersect/**
- tests/software/bedtools/intersect/** - tests/software/bedtools/intersect/**
bedtools_maskfasta:
- software/bedtools/maskfasta/**
- tests/software/bedtools/maskfasta/**
bedtools_merge: bedtools_merge:
- software/bedtools/merge/** - software/bedtools/merge/**
- tests/software/bedtools/merge/** - tests/software/bedtools/merge/**

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@ -0,0 +1,59 @@
/*
* -----------------------------------------------------
* Utility functions used in nf-core DSL2 module files
* -----------------------------------------------------
*/
/*
* Extract name of software tool from process name using $task.process
*/
def getSoftwareName(task_process) {
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
}
/*
* Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
*/
def initOptions(Map args) {
def Map options = [:]
options.args = args.args ?: ''
options.args2 = args.args2 ?: ''
options.publish_by_id = args.publish_by_id ?: false
options.publish_dir = args.publish_dir ?: ''
options.publish_files = args.publish_files
options.suffix = args.suffix ?: ''
return options
}
/*
* Tidy up and join elements of a list to return a path string
*/
def getPathFromList(path_list) {
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
return paths.join('/')
}
/*
* Function to save/publish module results
*/
def saveFiles(Map args) {
if (!args.filename.endsWith('.version.txt')) {
def ioptions = initOptions(args.options)
def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
if (ioptions.publish_by_id) {
path_list.add(args.publish_id)
}
if (ioptions.publish_files instanceof Map) {
for (ext in ioptions.publish_files) {
if (args.filename.endsWith(ext.key)) {
def ext_list = path_list.collect()
ext_list.add(ext.value)
return "${getPathFromList(ext_list)}/$args.filename"
}
}
} else if (ioptions.publish_files == null) {
return "${getPathFromList(path_list)}/$args.filename"
}
}
}

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@ -0,0 +1,41 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options)
process BEDTOOLS_MASKFASTA {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id: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--hc088bd4_0"
} else {
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
}
input:
tuple val(meta), path(bed)
path fasta
output:
tuple val(meta), path("*.fa"), emit: fasta
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
bedtools \\
maskfasta \\
$options.args \\
-fi $fasta \\
-bed $bed \\
-fo ${prefix}.fa
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
"""
}

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@ -0,0 +1,64 @@
name: bedtools_maskfasta
description: masks sequences in a FASTA file based on intervals defined in a feature file.
keywords:
- bed
- fasta
- maskfasta
tools:
- bedtools:
description: |
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html
params:
- outdir:
type: string
description: |
The pipeline's output directory. By default, the module will
output files into `$params.outdir/<SOFTWARE>`
- publish_dir_mode:
type: string
description: |
Value for the Nextflow `publishDir` mode parameter.
Available: symlink, rellink, link, copy, copyNoFollow, move.
- enable_conda:
type: boolean
description: |
Run the module with Conda using the software specified
via the `conda` directive
- singularity_pull_docker_container:
type: boolean
description: |
Instead of directly downloading Singularity images for use with Singularity,
force the workflow to pull and convert Docker containers instead.
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Bed feature file
pattern: "*.{bed}"
- fasta:
type: file
description: Input fasta file
pattern: "*.{fa,fasta}"
output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- fasta:
type: file
description: Output masked fasta file
pattern: "*.{fa}"
- version:
type: file
description: File containing software version
pattern: "*.{version.txt}"
authors:
- "@joseespinosa"
- "@drpatelh"

1
tests/data/bed/C.bed Normal file
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@ -0,0 +1 @@
gi|170079663|ref|NC_010473.1| 1 100

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@ -0,0 +1,14 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BEDTOOLS_MASKFASTA } from '../../../../software/bedtools/maskfasta/main.nf' addParams( options: [:] )
workflow test_bedtools_maskfasta {
def input,fasta = []
bed = [ [ id:'test'],
file("${launchDir}/tests/data/bed/C.bed", checkIfExists: true) ]
fasta = [ file("${launchDir}/tests/data/fasta/E_coli/NC_010473.fa", checkIfExists: true) ]
BEDTOOLS_MASKFASTA( bed, fasta )
}

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@ -0,0 +1,8 @@
- name: bedtools maskfasta
command: nextflow run ./tests/software/bedtools/maskfasta -entry test_bedtools_maskfasta -c tests/config/nextflow.config
tags:
- bedtools
- bedtools_maskfasta
files:
- path: output/bedtools/test.fa
md5sum: 6ff45e409858b259090e1c04309adc3f