add filtlong (#919)

This commit is contained in:
Daniel Straub 2021-10-27 17:00:11 +02:00 committed by GitHub
parent 754db250a0
commit 12a3f80f33
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
6 changed files with 234 additions and 0 deletions

View file

@ -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// Do not publish versions.yml unless running from pytest workflow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"
}
}

43
modules/filtlong/main.nf Normal file
View file

@ -0,0 +1,43 @@
// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process FILTLONG {
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::filtlong=0.2.1" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0"
} else {
container "quay.io/biocontainers/filtlong:0.2.1--h9a82719_0"
}
input:
tuple val(meta), path(shortreads), path(longreads)
output:
tuple val(meta), path("${meta.id}_lr_filtlong.fastq.gz"), emit: reads
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def short_reads = meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
"""
filtlong \\
$short_reads \\
$options.args \\
$longreads \\
| gzip -n > ${prefix}_lr_filtlong.fastq.gz
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( filtlong --version | sed -e "s/Filtlong v//g" )
END_VERSIONS
"""
}

50
modules/filtlong/meta.yml Normal file
View file

@ -0,0 +1,50 @@
name: filtlong
description: Filtlong filters long reads based on quality measures or short read data.
keywords:
- nanopore
- quality control
- QC
- filtering
- long reads
- short reads
tools:
- filtlong:
description: Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
homepage: https://anaconda.org/bioconda/filtlong
documentation: None
tool_dev_url: https://github.com/rrwick/Filtlong
doi: ""
licence: ['GPL v3']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- shortreads:
type: file
description: fastq file
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
- longreads:
type: file
description: fastq file
pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
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"
- reads:
type: file
description: Filtered (compressed) fastq file
pattern: "*.fastq.gz"
authors:
- "@d4straub"

View file

@ -382,6 +382,10 @@ fgbio/sortbam:
- modules/fgbio/sortbam/**
- tests/modules/fgbio/sortbam/**
filtlong:
- modules/filtlong/**
- tests/modules/filtlong/**
flash:
- modules/flash/**
- tests/modules/flash/**

View file

@ -0,0 +1,36 @@
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { FILTLONG } from '../../../modules/filtlong/main.nf' addParams( options: [:] )
workflow test_filtlong {
input = [ [ id:'test', single_end:false ], // meta map
[],
[ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
]
FILTLONG ( input )
}
workflow test_filtlong_illumina_se {
input = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ],
[ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
]
FILTLONG ( input )
}
workflow test_filtlong_illumina_pe {
input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
[ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
]
FILTLONG ( input )
}

View file

@ -0,0 +1,23 @@
- name: filtlong test_filtlong
command: nextflow run tests/modules/filtlong -entry test_filtlong -c tests/config/nextflow.config
tags:
- filtlong
files:
- path: output/filtlong/test_lr_filtlong.fastq.gz
md5sum: 7029066c27ac6f5ef18d660d5741979a
- name: filtlong test_filtlong_illumina_se
command: nextflow run tests/modules/filtlong -entry test_filtlong_illumina_se -c tests/config/nextflow.config
tags:
- filtlong
files:
- path: output/filtlong/test_lr_filtlong.fastq.gz
md5sum: 7029066c27ac6f5ef18d660d5741979a
- name: filtlong test_filtlong_illumina_pe
command: nextflow run tests/modules/filtlong -entry test_filtlong_illumina_pe -c tests/config/nextflow.config
tags:
- filtlong
files:
- path: output/filtlong/test_lr_filtlong.fastq.gz
md5sum: 7029066c27ac6f5ef18d660d5741979a