add emmtyper module (#1028)

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
This commit is contained in:
Robert A. Petit III 2021-11-08 12:43:15 -07:00 committed by GitHub
parent 316aedaaa6
commit 8ca8da46c2
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//
// 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// Do not publish versions.yml unless running from pytest workflow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"
}
}

41
modules/emmtyper/main.nf Normal file
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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
params.options = [:]
options = initOptions(params.options)
process EMMTYPER {
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::emmtyper=0.2.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/emmtyper:0.2.0--py_0"
} else {
container "quay.io/biocontainers/emmtyper:0.2.0--py_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}"
"""
emmtyper \\
$options.args \\
$fasta \\
> ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( echo \$(emmtyper --version 2>&1) | sed 's/^.*emmtyper v//' )
END_VERSIONS
"""
}

43
modules/emmtyper/meta.yml Normal file
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name: emmtyper
description: EMM typing of Streptococcus pyogenes assemblies
keywords:
- fasta
- Streptococcus pyogenes
- typing
tools:
- emmtyper:
description: Streptococcus pyogenes in silico EMM typer
homepage: https://github.com/MDU-PHL/emmtyper
documentation: https://github.com/MDU-PHL/emmtyper
tool_dev_url: https://github.com/MDU-PHL/emmtyper
doi: ""
licence: ['GNU General Public v3 (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"

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@ -362,6 +362,10 @@ dshbio/splitgff3:
- modules/dshbio/splitgff3/**
- tests/modules/dshbio/splitgff3/**
emmtyper:
- modules/emmtyper/**
- tests/modules/emmtyper/**
ensemblvep:
- modules/ensemblvep/**
- tests/modules/ensemblvep/**

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { EMMTYPER } from '../../../modules/emmtyper/main.nf' addParams( options: [:] )
workflow test_emmtyper {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
EMMTYPER ( input )
}

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- name: emmtyper test_emmtyper
command: nextflow run tests/modules/emmtyper -entry test_emmtyper -c tests/config/nextflow.config
tags:
- emmtyper
files:
- path: output/emmtyper/test.tsv
md5sum: c727ba859adec9ca8ff0e091ecf79c62