diff --git a/modules/kronatools/kronadb/functions.nf b/modules/kronatools/kronadb/functions.nf new file mode 100644 index 00000000..85628ee0 --- /dev/null +++ b/modules/kronatools/kronadb/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{ + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + + // Do not publish versions.yml unless running from pytest workflow + if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) { + return null + } + if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)}/$args.filename" + } +} diff --git a/modules/kronatools/kronadb/main.nf b/modules/kronatools/kronadb/main.nf new file mode 100644 index 00000000..7dee12d0 --- /dev/null +++ b/modules/kronatools/kronadb/main.nf @@ -0,0 +1,35 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process KRONATOOLS_KRONADB { + label 'process_low' + publishDir "${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::krona=2.7.1" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5" + } else { + container "quay.io/biocontainers/krona:2.7.1--pl526_5" + } + input: + + output: + path 'taxonomy/taxonomy.tab', emit: db + path "versions.yml" , emit: versions + + script: + def VERSION='2.7.1' + """ + ktUpdateTaxonomy.sh taxonomy + + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: $VERSION + END_VERSIONS + """ +} diff --git a/modules/kronatools/kronadb/meta.yml b/modules/kronatools/kronadb/meta.yml new file mode 100644 index 00000000..5a637949 --- /dev/null +++ b/modules/kronatools/kronadb/meta.yml @@ -0,0 +1,30 @@ +name: kronatools_kronadb +description: KronaTools Update Taxonomy downloads a taxonomy database +keywords: + - database + - taxonomy + - krona +tools: + - kronatools: + description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. + homepage: https://github.com/marbl/Krona/wiki/KronaTools + documentation: https://github.com/marbl/Krona/wiki/Installing + tool_dev_url: + doi: https://doi.org/10.1186/1471-2105-12-385 + licence: + +input: + - none: There is no input. This module downloads a pre-built taxonomy database for use with Krona Tools. + +output: + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - db: + type: file + description: A TAB separated file that contains a taxonomy database. + pattern: "*.{tab}" + +authors: + - "@mjakobs" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 794c7f4d..fb239baf 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -702,6 +702,10 @@ kraken2/kraken2: - modules/untar/** - tests/modules/kraken2/kraken2/** +kronatools/kronadb: + - modules/kronatools/kronadb/** + - tests/modules/kronatools/kronadb/** + last/dotplot: - modules/last/dotplot/** - tests/modules/last/dotplot/** diff --git a/tests/modules/kronatools/kronadb/main.nf b/tests/modules/kronatools/kronadb/main.nf new file mode 100644 index 00000000..90b6e30c --- /dev/null +++ b/tests/modules/kronatools/kronadb/main.nf @@ -0,0 +1,9 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { KRONATOOLS_KRONADB } from '../../../../modules/kronatools/kronadb/main.nf' addParams( options: [:] ) + +workflow test_kronatools_kronadb { + KRONATOOLS_KRONADB ( ) +} diff --git a/tests/modules/kronatools/kronadb/test.yml b/tests/modules/kronatools/kronadb/test.yml new file mode 100644 index 00000000..3f346a9d --- /dev/null +++ b/tests/modules/kronatools/kronadb/test.yml @@ -0,0 +1,7 @@ +- name: kronatools kronadb test_kronatools_kronadb + command: nextflow run tests/modules/kronatools/kronadb -entry test_kronatools_kronadb -c tests/config/nextflow.config + tags: + - kronatools + - kronatools/kronadb + files: + - path: output/kronatools/taxonomy/taxonomy.tab