From 8d9e8ae839df0e6f0070f8615e69f3103f9f3359 Mon Sep 17 00:00:00 2001 From: avantonder Date: Mon, 15 Nov 2021 17:26:37 +0000 Subject: [PATCH] Add Medaka module (#992) * add racon * add medaka module * add medaka module * add medaka module * add medaka module * add medaka module * add medaka module * Indentation * Apply suggestions from code review Co-authored-by: FriederikeHanssen * Update main.nf * Update main.nf * Apply suggestions from code review Co-authored-by: FriederikeHanssen Co-authored-by: Harshil Patel --- modules/medaka/functions.nf | 78 +++++++++++++++++++++++++++++++++ modules/medaka/main.nf | 47 ++++++++++++++++++++ modules/medaka/meta.yml | 47 ++++++++++++++++++++ tests/config/pytest_modules.yml | 4 ++ tests/modules/medaka/main.nf | 16 +++++++ tests/modules/medaka/test.yml | 7 +++ 6 files changed, 199 insertions(+) create mode 100644 modules/medaka/functions.nf create mode 100644 modules/medaka/main.nf create mode 100644 modules/medaka/meta.yml create mode 100644 tests/modules/medaka/main.nf create mode 100644 tests/modules/medaka/test.yml diff --git a/modules/medaka/functions.nf b/modules/medaka/functions.nf new file mode 100644 index 00000000..85628ee0 --- /dev/null +++ b/modules/medaka/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)}/$args.filename" + } +} diff --git a/modules/medaka/main.nf b/modules/medaka/main.nf new file mode 100644 index 00000000..a0db4150 --- /dev/null +++ b/modules/medaka/main.nf @@ -0,0 +1,47 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process MEDAKA { + tag "$meta.id" + label 'process_high' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::medaka=1.4.4" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/medaka:1.4.4--py38h130def0_0" + } else { + container "quay.io/biocontainers/medaka:1.4.4--py38h130def0_0" + } + + input: + tuple val(meta), path(reads), path(assembly) + + output: + tuple val(meta), path("*.fa.gz"), emit: assembly + path "versions.yml" , emit: versions + + script: + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + medaka_consensus \\ + -t $task.cpus \\ + $options.args \\ + -i $reads \\ + -d $assembly \\ + -o ./ + + mv consensus.fasta ${prefix}.fa + + gzip -n ${prefix}.fa + + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$( medaka --version 2>&1 | sed 's/medaka //g' ) + END_VERSIONS + """ +} diff --git a/modules/medaka/meta.yml b/modules/medaka/meta.yml new file mode 100644 index 00000000..d194464f --- /dev/null +++ b/modules/medaka/meta.yml @@ -0,0 +1,47 @@ +name: medaka +description: A tool to create consensus sequences and variant calls from nanopore sequencing data +keywords: + - assembly + - polishing + - nanopore +tools: + - medaka: + description: Neural network sequence error correction. + homepage: https://nanoporetech.github.io/medaka/index.html + documentation: https://nanoporetech.github.io/medaka/index.html + tool_dev_url: https://github.com/nanoporetech/medaka + doi: "" + licence: ['Mozilla Public License 2.0'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input nanopore fasta/FastQ files + pattern: "*.{fasta,fa,fastq,fastq.gz,fq,fq.gz}" + - assembly: + type: file + description: Genome assembly + pattern: "*.{fasta,fa}" + +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" + - assembly: + type: file + description: Polished genome assembly + pattern: "*.fa.gz" + +authors: + - "@avantonder" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 6c0b7b34..b286f114 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -822,6 +822,10 @@ maxbin2: - modules/maxbin2/** - tests/modules/maxbin2/** +medaka: + - modules/medaka/** + - tests/modules/medaka/** + megahit: - modules/megahit/** - tests/modules/megahit/** diff --git a/tests/modules/medaka/main.nf b/tests/modules/medaka/main.nf new file mode 100644 index 00000000..300e086b --- /dev/null +++ b/tests/modules/medaka/main.nf @@ -0,0 +1,16 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { MEDAKA } from '../../../modules/medaka/main.nf' addParams( options: [suffix:'.polished.genome'] ) + +workflow test_medaka { + + input = [ + [ id:'test', single_end:true ], // meta map + file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + + MEDAKA ( input ) +} diff --git a/tests/modules/medaka/test.yml b/tests/modules/medaka/test.yml new file mode 100644 index 00000000..9ce5521e --- /dev/null +++ b/tests/modules/medaka/test.yml @@ -0,0 +1,7 @@ +- name: medaka test_medaka + command: nextflow run ./tests/modules/medaka -entry test_medaka -c tests/config/nextflow.config + tags: + - medaka + files: + - path: output/medaka/test.polished.genome.fa.gz + md5sum: f42303f1d6c2c79175faeb00e10b9a6e \ No newline at end of file