diff --git a/modules/porechop/functions.nf b/modules/porechop/functions.nf new file mode 100644 index 00000000..85628ee0 --- /dev/null +++ b/modules/porechop/functions.nf @@ -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{ + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if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)}/$args.filename" + } +} diff --git a/modules/porechop/main.nf b/modules/porechop/main.nf new file mode 100644 index 00000000..cf564938 --- /dev/null +++ b/modules/porechop/main.nf @@ -0,0 +1,42 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process PORECHOP { + tag "$meta.id" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::porechop=0.2.4" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/porechop:0.2.4--py39h7cff6ad_2" + } else { + container "quay.io/biocontainers/porechop:0.2.4--py38h8c62d01_2" + } + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("*.fastq.gz") , emit: reads + path "versions.yml" , emit: versions + + script: + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + porechop \\ + -i ${reads} \\ + -t ${task.cpus} \\ + ${options.args} \\ + -o ${prefix}.fastq.gz + + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$( porechop --version ) + END_VERSIONS + """ +} diff --git a/modules/porechop/meta.yml b/modules/porechop/meta.yml new file mode 100644 index 00000000..81399d28 --- /dev/null +++ b/modules/porechop/meta.yml @@ -0,0 +1,50 @@ +name: porechop +description: Adapter removal and demultiplexing of Oxford Nanopore reads +keywords: + - adapter + - nanopore + - demultiplexing +tools: + - porechop: + description: Adapter removal and demultiplexing of Oxford Nanopore reads + homepage: "https://github.com/rrwick/Porechop" + documentation: "https://github.com/rrwick/Porechop" + tool_dev_url: "https://github.com/rrwick/Porechop" + doi: "10.1099/mgen.0.000132" + licence: ["GPL v3"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: fastq/fastq.gz file + pattern: "*.{fastq,fastq.gz,fq,fq.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: Demultiplexed and/or adapter-trimmed fastq.gz file + pattern: "*.{fastq.gz}" + +authors: + - "@ggabernet" + - "@jasmezz" + - "@d4straub" + - "@LaurenceKuhl" + - "@SusiJo" + - "@jonasscheid" + - "@jonoave" + - "@GokceOGUZ" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index e6913ef3..c3aa3c93 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -863,6 +863,10 @@ plink/vcf: - modules/plink/vcf/** - tests/modules/plink/vcf/** +porechop: + - modules/porechop/** + - tests/modules/porechop/** + preseq/lcextrap: - modules/preseq/lcextrap/** - tests/modules/preseq/lcextrap/** diff --git a/tests/modules/porechop/main.nf b/tests/modules/porechop/main.nf new file mode 100644 index 00000000..b6d7bafa --- /dev/null +++ b/tests/modules/porechop/main.nf @@ -0,0 +1,13 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { PORECHOP } from '../../../modules/porechop/main.nf' addParams( options: [args: '', suffix: '_porechop'] ) + +workflow test_porechop { + + input = [ [ id:'test', single_end:true ], // meta map + file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true) ] + + PORECHOP ( input ) +} diff --git a/tests/modules/porechop/test.yml b/tests/modules/porechop/test.yml new file mode 100644 index 00000000..b37a7ec4 --- /dev/null +++ b/tests/modules/porechop/test.yml @@ -0,0 +1,7 @@ +- name: porechop test_porechop + command: nextflow run tests/modules/porechop -entry test_porechop -c tests/config/nextflow.config + tags: + - porechop + files: + - path: output/porechop/test_porechop.fastq.gz + md5sum: 08f314ae9f162c8dcc27e5b513d2064d