Bbmap index (#683)

BBMap index module
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Daniel Lundin 2021-09-03 09:28:28 +02:00 committed by GitHub
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6 changed files with 180 additions and 1 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 BBMAP_INDEX {
tag "$fasta"
label 'process_long'
publishDir "${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::bbmap=38.92" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bbmap:38.92--he522d1c_0"
} else {
container "quay.io/biocontainers/bbmap:38.92--he522d1c_0"
}
input:
tuple val(meta), path(fasta)
output:
tuple val(meta), path('ref') , emit: index
path "*.version.txt" , emit: version
script:
def software = getSoftwareName(task.process)
"""
bbmap.sh \\
ref=${fasta} \\
$options.args \\
threads=$task.cpus \\
-Xmx${task.memory.toGiga()}g
echo \$(bbversion.sh) > ${software}.version.txt
"""
}

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name: bbmap_index
description: This module calls bbmap.sh to create an index from a fasta file, ready to be used by bbmap.sh in mapping mode.
keywords:
- mapping
- index
- fasta
tools:
- bbmap:
description: BBMap is a short read aligner, as well as various other bioinformatic tools.
homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/
tool_dev_url: None
doi: ""
licence: ['UC-LBL license (see package)']
input:
- meta:
type: map
description: |
Groovy Map containing optional parameters to bbmap.sh
e.g. [ id:'test', single_end:false ]
- fasta:
type: fasta
description: fasta formatted file with nucleotide sequences
pattern: "*.{fna,fa,fasta}"
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}"
- db:
type: directory
description: Directory with index files
pattern: "ref"
authors:
- "@daniellundin"

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@ -30,6 +30,10 @@ bbmap/bbduk:
- modules/bbmap/bbduk/**
- tests/modules/bbmap/bbduk/**
bbmap/index:
- modules/bbmap/index/**
- tests/modules/bbmap/index/**
bcftools/concat:
- modules/bcftools/concat/**
- tests/modules/bcftools/concat/**
@ -245,7 +249,7 @@ deeptools/plotprofile:
delly/call:
- modules/delly/call/**
- tests/modules/delly/call/**
dragonflye:
- modules/dragonflye/**
- tests/modules/dragonflye/**

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BBMAP_INDEX } from '../../../../modules/bbmap/index/main.nf' addParams( options: [:] )
workflow test_bbmap_index {
input = [ [ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
BBMAP_INDEX ( input )
}

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## TODO nf-core: Please run the following command to build this file:
# nf-core modules create-test-yml bbmap/index
- name: bbmap index
command: nextflow run ./tests/modules/bbmap/index -entry test_bbmap_index -c tests/config/nextflow.config
tags:
- bbmap
- bbmap/index
files:
- path: output/bbmap/ref/genome/1/chr1.chrom.gz
md5sum: fc20702f3378836f06d4104b9cd88918
- path: output/bbmap/ref/index/1/chr1_index_k13_c15_b1.block
md5sum: 9f0d9a7413c1d2c16cc24555b2381163