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add filtlong (#919)
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6 changed files with 234 additions and 0 deletions
78
modules/filtlong/functions.nf
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78
modules/filtlong/functions.nf
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//
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// Utility functions used in nf-core DSL2 module files
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//
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//
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// Extract name of software tool from process name using $task.process
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//
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def getSoftwareName(task_process) {
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return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
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}
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//
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// Extract name of module from process name using $task.process
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//
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def getProcessName(task_process) {
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return task_process.tokenize(':')[-1]
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}
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//
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// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
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//
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def initOptions(Map args) {
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def Map options = [:]
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options.args = args.args ?: ''
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options.args2 = args.args2 ?: ''
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options.args3 = args.args3 ?: ''
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options.publish_by_meta = args.publish_by_meta ?: []
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options.publish_dir = args.publish_dir ?: ''
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options.publish_files = args.publish_files
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options.suffix = args.suffix ?: ''
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return options
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}
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//
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// Tidy up and join elements of a list to return a path string
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//
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def getPathFromList(path_list) {
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def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries
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paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
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return paths.join('/')
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}
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//
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// Function to save/publish module results
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//
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def saveFiles(Map args) {
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def ioptions = initOptions(args.options)
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def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
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// Do not publish versions.yml unless running from pytest workflow
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if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
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return null
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}
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if (ioptions.publish_by_meta) {
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def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
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for (key in key_list) {
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if (args.meta && key instanceof String) {
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def path = key
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if (args.meta.containsKey(key)) {
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path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]
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}
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path = path instanceof String ? path : ''
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path_list.add(path)
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}
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}
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}
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if (ioptions.publish_files instanceof Map) {
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for (ext in ioptions.publish_files) {
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if (args.filename.endsWith(ext.key)) {
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def ext_list = path_list.collect()
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ext_list.add(ext.value)
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return "${getPathFromList(ext_list)}/$args.filename"
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}
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}
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} else if (ioptions.publish_files == null) {
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return "${getPathFromList(path_list)}/$args.filename"
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}
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}
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43
modules/filtlong/main.nf
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43
modules/filtlong/main.nf
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process FILTLONG {
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tag "$meta.id"
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label 'process_low'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::filtlong=0.2.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/filtlong:0.2.1--h9a82719_0"
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} else {
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container "quay.io/biocontainers/filtlong:0.2.1--h9a82719_0"
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}
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input:
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tuple val(meta), path(shortreads), path(longreads)
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output:
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tuple val(meta), path("${meta.id}_lr_filtlong.fastq.gz"), emit: reads
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def short_reads = meta.single_end ? "-1 $shortreads" : "-1 ${shortreads[0]} -2 ${shortreads[1]}"
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"""
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filtlong \\
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$short_reads \\
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$options.args \\
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$longreads \\
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| gzip -n > ${prefix}_lr_filtlong.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$( filtlong --version | sed -e "s/Filtlong v//g" )
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END_VERSIONS
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"""
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}
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50
modules/filtlong/meta.yml
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50
modules/filtlong/meta.yml
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name: filtlong
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description: Filtlong filters long reads based on quality measures or short read data.
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keywords:
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- nanopore
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- quality control
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- QC
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- filtering
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- long reads
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- short reads
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tools:
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- filtlong:
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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.
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homepage: https://anaconda.org/bioconda/filtlong
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documentation: None
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tool_dev_url: https://github.com/rrwick/Filtlong
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doi: ""
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licence: ['GPL v3']
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input:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- shortreads:
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type: file
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description: fastq file
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pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
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- longreads:
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type: file
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description: fastq file
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pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
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output:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- versions:
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type: file
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description: File containing software versions
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pattern: "versions.yml"
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- reads:
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type: file
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description: Filtered (compressed) fastq file
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pattern: "*.fastq.gz"
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authors:
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- "@d4straub"
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@ -382,6 +382,10 @@ fgbio/sortbam:
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- modules/fgbio/sortbam/**
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- modules/fgbio/sortbam/**
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- tests/modules/fgbio/sortbam/**
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- tests/modules/fgbio/sortbam/**
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filtlong:
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- modules/filtlong/**
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- tests/modules/filtlong/**
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flash:
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flash:
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- modules/flash/**
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- modules/flash/**
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- tests/modules/flash/**
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- tests/modules/flash/**
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36
tests/modules/filtlong/main.nf
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36
tests/modules/filtlong/main.nf
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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
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[],
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[ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
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]
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FILTLONG ( input )
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}
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workflow test_filtlong_illumina_se {
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input = [ [ id:'test', single_end:true ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ],
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[ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
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]
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FILTLONG ( input )
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}
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workflow test_filtlong_illumina_pe {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ],
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[ file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ]
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]
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FILTLONG ( input )
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}
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23
tests/modules/filtlong/test.yml
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23
tests/modules/filtlong/test.yml
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- name: filtlong test_filtlong
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command: nextflow run tests/modules/filtlong -entry test_filtlong -c tests/config/nextflow.config
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tags:
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- filtlong
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files:
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- path: output/filtlong/test_lr_filtlong.fastq.gz
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md5sum: 7029066c27ac6f5ef18d660d5741979a
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- name: filtlong test_filtlong_illumina_se
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command: nextflow run tests/modules/filtlong -entry test_filtlong_illumina_se -c tests/config/nextflow.config
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tags:
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- filtlong
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files:
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- path: output/filtlong/test_lr_filtlong.fastq.gz
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md5sum: 7029066c27ac6f5ef18d660d5741979a
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- name: filtlong test_filtlong_illumina_pe
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command: nextflow run tests/modules/filtlong -entry test_filtlong_illumina_pe -c tests/config/nextflow.config
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tags:
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- filtlong
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files:
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- path: output/filtlong/test_lr_filtlong.fastq.gz
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md5sum: 7029066c27ac6f5ef18d660d5741979a
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