From bb7beff49740a7b92e851208b7e25875a909fe5c Mon Sep 17 00:00:00 2001 From: "Robert A. Petit III" Date: Tue, 5 Oct 2021 14:42:09 -0600 Subject: [PATCH] add hicap module (#772) * add hicap module * add info on optional inputs * fix typo * Update meta.yml * Update main.nf * Update meta.yml * Update modules/hicap/main.nf Co-authored-by: Harshil Patel * Update modules/hicap/main.nf Co-authored-by: Harshil Patel Co-authored-by: Harshil Patel --- modules/hicap/functions.nf | 78 +++++++++++++++++++++++++++++++++ modules/hicap/main.nf | 56 +++++++++++++++++++++++ modules/hicap/meta.yml | 59 +++++++++++++++++++++++++ tests/config/pytest_modules.yml | 4 ++ tests/modules/hicap/main.nf | 16 +++++++ tests/modules/hicap/test.yml | 10 +++++ 6 files changed, 223 insertions(+) create mode 100644 modules/hicap/functions.nf create mode 100644 modules/hicap/main.nf create mode 100644 modules/hicap/meta.yml create mode 100644 tests/modules/hicap/main.nf create mode 100644 tests/modules/hicap/test.yml diff --git a/modules/hicap/functions.nf b/modules/hicap/functions.nf new file mode 100644 index 00000000..85628ee0 --- /dev/null +++ b/modules/hicap/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)}/$args.filename" + } +} diff --git a/modules/hicap/main.nf b/modules/hicap/main.nf new file mode 100644 index 00000000..e2e70678 --- /dev/null +++ b/modules/hicap/main.nf @@ -0,0 +1,56 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions' + +params.options = [:] +options = initOptions(params.options) + +process HICAP { + tag "$meta.id" + label 'process_low' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) } + + conda (params.enable_conda ? "bioconda::hicap=1.0.3" : null) + if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { + container "https://depot.galaxyproject.org/singularity/hicap:1.0.3--py_0" + } else { + container "quay.io/biocontainers/hicap:1.0.3--py_0" + } + + input: + tuple val(meta), path(fasta) + path database_dir + path model_fp + + output: + tuple val(meta), path("*.gbk"), emit: gbk + tuple val(meta), path("*.svg"), emit: svg + tuple val(meta), path("*.tsv"), emit: tsv + path "versions.yml" , emit: versions + + script: + def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" + def database_args = database_dir ? "--database_dir ${database_dir}" : "" + def model_args = model_fp ? "--model_fp ${model_fp}" : "" + def is_compressed = fasta.getName().endsWith(".gz") ? true : false + def fasta_name = fasta.getName().replace(".gz", "") + """ + if [ "$is_compressed" == "true" ]; then + gzip -c -d $fasta > $fasta_name + fi + + hicap \\ + --query_fp $fasta_name \\ + $database_args \\ + $model_args \\ + $options.args \\ + --threads $task.cpus \\ + -o ./ + + cat <<-END_VERSIONS > versions.yml + ${getProcessName(task.process)}: + ${getSoftwareName(task.process)}: \$( echo \$( hicap --version 2>&1 ) | sed 's/^.*hicap //' ) + END_VERSIONS + """ +} diff --git a/modules/hicap/meta.yml b/modules/hicap/meta.yml new file mode 100644 index 00000000..275df665 --- /dev/null +++ b/modules/hicap/meta.yml @@ -0,0 +1,59 @@ +name: hicap +description: Identify cap locus serotype and structure in your Haemophilus influenzae assemblies +keywords: + - fasta + - serotype + - Haemophilus influenzae +tools: + - hicap: + description: In silico typing of the H. influenzae capsule locus + homepage: https://github.com/scwatts/hicap + documentation: https://github.com/scwatts/hicap + tool_dev_url: https://github.com/scwatts/hicap + doi: "https://doi.org/10.1128/JCM.00190-19" + 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 formatted assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - database_dir: + type: directory + description: Optional - Directory containing locus database + pattern: "*/*" + - model_fp: + type: file + description: Optional - Prodigal model to use for gene prediction + pattern: "*.{bin}" + +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" + - gbk: + type: file + description: GenBank file and cap locus annotations + pattern: "*.gbk" + - svg: + type: file + description: Visualization of annotated cap locus + pattern: "*.svg" + - tsv: + type: file + description: Detailed summary of cap locus annotations + pattern: "*.tsv" + +authors: + - "@rpetit3" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 7b010097..1cd98564 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -470,6 +470,10 @@ gunzip: - modules/gunzip/** - tests/modules/gunzip/** +hicap: + - modules/hicap/** + - tests/modules/hicap/** + hifiasm: - modules/hifiasm/** - tests/modules/hifiasm/** diff --git a/tests/modules/hicap/main.nf b/tests/modules/hicap/main.nf new file mode 100644 index 00000000..77c309a5 --- /dev/null +++ b/tests/modules/hicap/main.nf @@ -0,0 +1,16 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { HICAP } from '../../../modules/hicap/main.nf' addParams( options: [:] ) + +workflow test_hicap { + + input = [ [ id:'test', single_end:false ], // meta map + file("https://github.com/bactopia/bactopia-tests/raw/main/data/species-specific/haemophilus-influenzae/GCF_900478275.fna.gz", checkIfExists: true) ] + + database_dir = [] + model_fp = [] + + HICAP ( input, database_dir, model_fp ) +} diff --git a/tests/modules/hicap/test.yml b/tests/modules/hicap/test.yml new file mode 100644 index 00000000..8c8420fd --- /dev/null +++ b/tests/modules/hicap/test.yml @@ -0,0 +1,10 @@ +- name: hicap test_hicap + command: nextflow run tests/modules/hicap -entry test_hicap -c tests/config/nextflow.config + tags: + - hicap + files: + - path: output/hicap/GCF_900478275.gbk + md5sum: 562d026956903354ac80721f501335d4 + - path: output/hicap/GCF_900478275.svg + md5sum: 4fb94871dd0fdd8b4496049668176631 + - path: output/hicap/GCF_900478275.tsv