From 729d9ae450e166938435cd9da9d95bbe6ad9062c Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Sat, 6 Nov 2021 09:44:26 -0600 Subject: [PATCH] add meningotype module (#1022) Co-authored-by: Gregor Sturm --- modules/meningotype/functions.nf | 78 ++++++++++++++++++++++++++++++ modules/meningotype/main.nf | 41 ++++++++++++++++ modules/meningotype/meta.yml | 43 ++++++++++++++++ tests/config/pytest_modules.yml | 4 ++ tests/modules/meningotype/main.nf | 13 +++++ tests/modules/meningotype/test.yml | 7 +++ 6 files changed, 186 insertions(+) create mode 100644 modules/meningotype/functions.nf create mode 100644 modules/meningotype/main.nf create mode 100644 modules/meningotype/meta.yml create mode 100644 tests/modules/meningotype/main.nf create mode 100644 tests/modules/meningotype/test.yml diff --git a/modules/meningotype/functions.nf b/modules/meningotype/functions.nf new file mode 100644 index 00000000..85628ee0 --- /dev/null +++ b/modules/meningotype/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{ + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if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)}/$args.filename" + } +} diff --git a/modules/meningotype/main.nf b/modules/meningotype/main.nf new file mode 100644 index 00000000..4e779e8c --- /dev/null +++ b/modules/meningotype/main.nf @@ -0,0 +1,41 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process MENINGOTYPE { + tag "$meta.id" + label 'process_low' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::meningotype=0.8.5" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/meningotype:0.8.5--pyhdfd78af_0" + } else { + container "quay.io/biocontainers/meningotype:0.8.5--pyhdfd78af_0" + } + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("*.tsv"), emit: tsv + path "versions.yml" , emit: versions + + script: + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + meningotype \\ + $options.args \\ + $fasta \\ + > ${prefix}.tsv + + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$( echo \$(meningotype --version 2>&1) | sed 's/^.*meningotype v//' ) + END_VERSIONS + """ +} diff --git a/modules/meningotype/meta.yml b/modules/meningotype/meta.yml new file mode 100644 index 00000000..07c2ff5e --- /dev/null +++ b/modules/meningotype/meta.yml @@ -0,0 +1,43 @@ +name: meningotype +description: Serotyping of Neisseria meningitidis assemblies +keywords: + - fasta + - Neisseria meningitidis + - serotype +tools: + - meningotype: + description: In silico serotyping and finetyping (porA and fetA) of Neisseria meningitidis + homepage: https://github.com/MDU-PHL/meningotype + documentation: https://github.com/MDU-PHL/meningotype + tool_dev_url: https://github.com/MDU-PHL/meningotype + doi: "" + licence: ['GPL v3'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.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" + - tsv: + type: file + description: Tab-delimited result file + pattern: "*.tsv" + +authors: + - "@rpetit3" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 6d9d0d12..37da142b 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -766,6 +766,10 @@ megahit: - modules/megahit/** - tests/modules/megahit/** +meningotype: + - modules/meningotype/** + - tests/modules/meningotype/** + metaphlan3: - modules/metaphlan3/** - tests/modules/metaphlan3/** diff --git a/tests/modules/meningotype/main.nf b/tests/modules/meningotype/main.nf new file mode 100644 index 00000000..d660ec72 --- /dev/null +++ b/tests/modules/meningotype/main.nf @@ -0,0 +1,13 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { MENINGOTYPE } from '../../../modules/meningotype/main.nf' addParams( options: [:] ) + +workflow test_meningotype { + + input = [ [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + + MENINGOTYPE ( input ) +} diff --git a/tests/modules/meningotype/test.yml b/tests/modules/meningotype/test.yml new file mode 100644 index 00000000..c61e78a6 --- /dev/null +++ b/tests/modules/meningotype/test.yml @@ -0,0 +1,7 @@ +- name: meningotype test_meningotype + command: nextflow run tests/modules/meningotype -entry test_meningotype -c tests/config/nextflow.config + tags: + - meningotype + files: + - path: output/meningotype/test.tsv + md5sum: 25651bccb3d1c64cefcb7946fda30a6c