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add filtlong #919
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add filtlong #919
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// | ||
// Utility functions used in nf-core DSL2 module files | ||
// | ||
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// | ||
// Extract name of software tool from process name using $task.process | ||
// | ||
def getSoftwareName(task_process) { | ||
return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() | ||
} | ||
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// | ||
// Extract name of module from process name using $task.process | ||
// | ||
def getProcessName(task_process) { | ||
return task_process.tokenize(':')[-1] | ||
} | ||
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// | ||
// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules | ||
// | ||
def initOptions(Map args) { | ||
def Map options = [:] | ||
options.args = args.args ?: '' | ||
options.args2 = args.args2 ?: '' | ||
options.args3 = args.args3 ?: '' | ||
options.publish_by_meta = args.publish_by_meta ?: [] | ||
options.publish_dir = args.publish_dir ?: '' | ||
options.publish_files = args.publish_files | ||
options.suffix = args.suffix ?: '' | ||
return options | ||
} | ||
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// | ||
// Tidy up and join elements of a list to return a path string | ||
// | ||
def getPathFromList(path_list) { | ||
def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries | ||
paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes | ||
return paths.join('/') | ||
} | ||
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// | ||
// Function to save/publish module results | ||
// | ||
def saveFiles(Map args) { | ||
def ioptions = initOptions(args.options) | ||
def path_list = [ ioptions.publish_dir ?: args.publish_dir ] | ||
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// Do not publish versions.yml unless running from pytest workflow | ||
if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { | ||
return null | ||
} | ||
if (ioptions.publish_by_meta) { | ||
def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta | ||
for (key in key_list) { | ||
if (args.meta && key instanceof String) { | ||
def path = key | ||
if (args.meta.containsKey(key)) { | ||
path = args.meta[key] instanceof Boolean ? "${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)}/$args.filename" | ||
} | ||
} |
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// Import generic module functions | ||
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' | ||
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params.options = [:] | ||
options = initOptions(params.options) | ||
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process FILTLONG { | ||
tag "$meta.id" | ||
label 'process_low' | ||
publishDir "${params.outdir}", | ||
mode: params.publish_dir_mode, | ||
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } | ||
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conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null) | ||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { | ||
container "https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0" | ||
} else { | ||
container "quay.io/biocontainers/filtlong:0.2.1--h9a82719_0" | ||
} | ||
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input: | ||
tuple val(meta), path(shortreads), path(longreads) | ||
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output: | ||
tuple val(meta), path("${meta.id}_lr_filtlong.fastq.gz"), emit: reads | ||
path "versions.yml" , emit: versions | ||
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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 | ||
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cat <<-END_VERSIONS > versions.yml | ||
${getProcessName(task.process)}: | ||
${getSoftwareName(task.process)}: \$( filtlong --version | sed -e "s/Filtlong v//g" ) | ||
END_VERSIONS | ||
""" | ||
} |
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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'] | ||
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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}" | ||
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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" | ||
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authors: | ||
- "@d4straub" |
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#!/usr/bin/env nextflow | ||
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nextflow.enable.dsl = 2 | ||
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include { FILTLONG } from '../../../modules/filtlong/main.nf' addParams( options: [:] ) | ||
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workflow test_filtlong { | ||
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input = [ [ id:'test', single_end:false ], // meta map | ||
[], | ||
[ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ] | ||
] | ||
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FILTLONG ( input ) | ||
} | ||
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workflow test_filtlong_illumina_se { | ||
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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) ] | ||
] | ||
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FILTLONG ( input ) | ||
} | ||
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workflow test_filtlong_illumina_pe { | ||
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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) ] | ||
] | ||
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FILTLONG ( input ) | ||
} |
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- 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 | ||
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- 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 | ||
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- 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 |
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😢