Updated bedgraphtobigwig (be7b4318) · Commits · Chaos / Cutandrun

modules/nf-core/modules/ucsc/bedgraphtobigwig/functions.nf

+37 −28

Original line number	Diff line number	Diff line
		/*
		* -----------------------------------------------------
		* Utility functions used in nf-core DSL2 module files
		* -----------------------------------------------------
		*/
		//
		// Utility functions used in nf-core DSL2 module files
		//

		/*
		* Extract name of software tool from process name using $task.process
		*/
		//
		// 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
		*/
		//
		// 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.publish_by_id = args.publish_by_id ?: false
		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
		*/
		//
		// 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
		*/
		//
		// 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_id) {
		path_list.add(args.publish_id)
		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) {

modules/nf-core/modules/ucsc/bedgraphtobigwig/main.nf

+2 −2

Original line number	Diff line number	Diff line
		@@ -2,7 +2,7 @@
		include { initOptions; saveFiles; getSoftwareName } from './functions'

		params.options = [:]
		def options = initOptions(params.options)
		options = initOptions(params.options)

		def VERSION = '377'

		@@ -11,7 +11,7 @@ process UCSC_BEDGRAPHTOBIGWIG {
		label 'process_medium'
		publishDir "${params.outdir}",
		mode: params.publish_dir_mode,
		saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
		saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }

		conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
		if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {

modules/nf-core/modules/ucsc/bedgraphtobigwig/meta.yml

0 → 100644

+46 −0

Original line number	Diff line number	Diff line
		name: ucsc_bedgraphtobigwig
		description: Convert a bedGraph file to bigWig format.
		keywords:
		- bedgraph
		- bigwig
		tools:
		- ucsc:
		description: Convert a bedGraph file to bigWig format.
		homepage: None
		documentation: None
		tool_dev_url: None
		doi: ""
		licence: ["varies; see http://genome.ucsc.edu/license"]

		input:
		- meta:
		type: map
		description: \|
		Groovy Map containing sample information
		e.g. [ id:'test', single_end:false ]
		- bedgraph:
		type: file
		description: bedGraph file
		pattern: "*.{bedGraph}"
		- sizes:
		type: file
		description: chromosome sizes file
		pattern: "*.{sizes}"

		output:
		- meta:
		type: map
		description: \|
		Groovy Map containing sample information
		e.g. [ id:'test', single_end:false ]
		- version:
		type: file
		description: File containing software version
		pattern: "*.{version.txt}"
		- bigwig:
		type: file
		description: bigWig file
		pattern: "*.{bigWig}"

		authors:
		- "@drpatelh"

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