From 18402890683bb34a575840827827db364a67b336 Mon Sep 17 00:00:00 2001 From: Abhinav Sharma Date: Thu, 16 Sep 2021 12:42:23 +0200 Subject: [PATCH] module for `agrvate` (#693) * initiate agrvate module * remove todos [ci skip] * remove todos and fix containers [ci skip] * ready for testing Co-authored-by: Harshil Patel --- modules/agrvate/functions.nf | 68 +++++++++++++++++++++++++++++++++ modules/agrvate/main.nf | 39 +++++++++++++++++++ modules/agrvate/meta.yml | 46 ++++++++++++++++++++++ tests/config/pytest_modules.yml | 4 ++ tests/modules/agrvate/main.nf | 13 +++++++ tests/modules/agrvate/test.yml | 7 ++++ 6 files changed, 177 insertions(+) create mode 100644 modules/agrvate/functions.nf create mode 100644 modules/agrvate/main.nf create mode 100644 modules/agrvate/meta.yml create mode 100644 tests/modules/agrvate/main.nf create mode 100644 tests/modules/agrvate/test.yml diff --git a/modules/agrvate/functions.nf b/modules/agrvate/functions.nf new file mode 100644 index 00000000..da9da093 --- /dev/null +++ b/modules/agrvate/functions.nf @@ -0,0 +1,68 @@ +// +// Utility functions used in nf-core DSL2 module files +// + +// +// Extract name of software tool from process name using $task.process +// +def getSoftwareName(task_process) { + return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase() +} + +// +// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules +// +def initOptions(Map args) { + def Map options = [:] + options.args = args.args ?: '' + options.args2 = args.args2 ?: '' + options.args3 = args.args3 ?: '' + options.publish_by_meta = args.publish_by_meta ?: [] + options.publish_dir = args.publish_dir ?: '' + options.publish_files = args.publish_files + options.suffix = args.suffix ?: '' + return options +} + +// +// Tidy up and join elements of a list to return a path string +// +def getPathFromList(path_list) { + def paths = path_list.findAll { item -> !item?.trim().isEmpty() } // Remove empty entries + paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes + return paths.join('/') +} + +// +// Function to save/publish module results +// +def saveFiles(Map args) { + if (!args.filename.endsWith('.version.txt')) { + def ioptions = initOptions(args.options) + def path_list = [ ioptions.publish_dir ?: args.publish_dir ] + if (ioptions.publish_by_meta) { + def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta + for (key in key_list) { + if (args.meta && key instanceof String) { + def path = key + if (args.meta.containsKey(key)) { + path = args.meta[key] instanceof Boolean ? "${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)}/$args.filename" + } + } +} diff --git a/modules/agrvate/main.nf b/modules/agrvate/main.nf new file mode 100644 index 00000000..bbbd9fa0 --- /dev/null +++ b/modules/agrvate/main.nf @@ -0,0 +1,39 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process AGRVATE { + tag "$meta.id" + label 'process_low' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::agrvate=1.0" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/agrvate:1.0--hdfd78af_0" + } else { + container "quay.io/biocontainers/agrvate:1.0--hdfd78af_0" + } + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("${fasta.baseName}-results/${fasta.baseName}-summary.tab"), emit: summary + path "${fasta.baseName}-results" , emit: results_dir + path "*.version.txt" , emit: version + + script: + def software = getSoftwareName(task.process) + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + """ + agrvate \\ + $options.args \\ + -i $fasta + + echo \$(agrvate -v 2>&1) | sed 's/agrvate //;' > ${software}.version.txt + """ +} diff --git a/modules/agrvate/meta.yml b/modules/agrvate/meta.yml new file mode 100644 index 00000000..97aa5f58 --- /dev/null +++ b/modules/agrvate/meta.yml @@ -0,0 +1,46 @@ +name: agrvate +description: Rapid identification of Staphylococcus aureus agr locus type and agr operon variants +keywords: + - fasta + - virulence + - Staphylococcus aureus +tools: + - agrvate: + description: Rapid identification of Staphylococcus aureus agr locus type and agr operon variants. + homepage: https://github.com/VishnuRaghuram94/AgrVATE + documentation: https://github.com/VishnuRaghuram94/AgrVATE + tool_dev_url: https://github.com/VishnuRaghuram94/AgrVATE + doi: "" + licence: ['MIT'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A Staphylococcus aureus fasta file. + pattern: "*.fasta" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - summary: + type: file + description: A summary of the agrvate assessement + pattern: "*-summary.tab" + - results_dir: + type: directory + description: Results of the agrvate assessement + pattern: "*-results" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@abhi18av" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 3105e590..164e7d5d 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -6,6 +6,10 @@ adapterremoval: - modules/adapterremoval/** - tests/modules/adapterremoval/** +agrvate: + - modules/agrvate/** + - tests/modules/agrvate/** + allelecounter: - modules/allelecounter/** - tests/modules/allelecounter/** diff --git a/tests/modules/agrvate/main.nf b/tests/modules/agrvate/main.nf new file mode 100644 index 00000000..58058fe3 --- /dev/null +++ b/tests/modules/agrvate/main.nf @@ -0,0 +1,13 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { AGRVATE } from '../../../modules/agrvate/main.nf' addParams( options: ["args": "--mummer"] ) + +workflow test_agrvate { + + input = [ [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + + AGRVATE ( input ) +} diff --git a/tests/modules/agrvate/test.yml b/tests/modules/agrvate/test.yml new file mode 100644 index 00000000..ec413663 --- /dev/null +++ b/tests/modules/agrvate/test.yml @@ -0,0 +1,7 @@ +- name: agrvate + command: nextflow run ./tests/modules/agrvate -entry test_agrvate -c tests/config/nextflow.config + tags: + - agrvate + files: + - path: output/agrvate/genome-results/genome-summary.tab + md5sum: 781a9e5fc6ebc9f90ddfe8753d1633db