add scoary module (#1034)

Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
This commit is contained in:
Robert A. Petit III 2021-11-06 09:34:39 -06:00 committed by GitHub
parent 02932973fa
commit 22aa168622
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6 changed files with 202 additions and 0 deletions

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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// Do not publish versions.yml unless running from pytest workflow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"
}
}

45
modules/scoary/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 SCOARY {
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::scoary=1.6.16" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/scoary:1.6.16--py_2"
} else {
container "quay.io/biocontainers/scoary:1.6.16--py_2"
}
input:
tuple val(meta), path(genes), path(traits)
path(tree)
output:
tuple val(meta), path("*.csv"), emit: csv
path "versions.yml" , emit: versions
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def newick_tree = tree ? "-n ${tree}" : ""
"""
scoary \\
$options.args \\
--no-time \\
--threads $task.cpus \\
--traits $traits \\
--genes $genes
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$( scoary --version 2>&1 )
END_VERSIONS
"""
}

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modules/scoary/meta.yml Normal file
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name: scoary
description: Use pangenome outputs for GWAS
keywords:
- gwas
- pangenome
- prokaryote
tools:
- scoary:
description: Microbial pan-GWAS using the output from Roary
homepage: https://github.com/AdmiralenOla/Scoary
documentation: https://github.com/AdmiralenOla/Scoary
tool_dev_url: https://github.com/AdmiralenOla/Scoary
doi: "10.1186/s13059-016-1108-8"
licence: ['GPL v3']
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- genes:
type: file
description: A presence/absence matrix of genes in the pan-genome
pattern: "*.csv"
- traits:
type: file
description: A CSV file containing trait information per-sample
pattern: "*.csv"
- tree:
type: file
description: A Newick formtted tree for phylogenetic analyses
pattern: "*.{dnd,nwk,treefile}"
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"
- csv:
type: file
description: Gene associations in a CSV file per trait
pattern: "*.csv"
authors:
- "@rpetit3"

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@ -1083,6 +1083,10 @@ samtools/view:
- modules/samtools/view/**
- tests/modules/samtools/view/**
scoary:
- modules/scoary/**
- tests/modules/scoary/**
seacr/callpeak:
- modules/seacr/callpeak/**
- tests/modules/seacr/callpeak/**

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SCOARY } from '../../../modules/scoary/main.nf' addParams( options: [:] )
workflow test_scoary {
input = [ [ id:'test', single_end:false ], // meta map
file("https://github.com/AdmiralenOla/Scoary/raw/master/scoary/exampledata/Gene_presence_absence.csv", checkIfExists: true),
file("https://github.com/AdmiralenOla/Scoary/raw/master/scoary/exampledata/Tetracycline_resistance.csv", checkIfExists: true) ]
tree = []
SCOARY ( input, tree)
}

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- name: scoary test_scoary
command: nextflow run tests/modules/scoary -entry test_scoary -c tests/config/nextflow.config
tags:
- scoary
files:
- path: output/scoary/Bogus_trait.results.csv
md5sum: 9550c692bbe6ff0ac844357bfabb809b
- path: output/scoary/Tetracycline_resistance.results.csv
md5sum: a87740818ab4de69a758fc75d7b879dd