Updated deeptools plot heatmap (8985a206) · Commits · Chaos / Cutandrun

modules/nf-core/modules/deeptools/plotheatmap/functions.nf

+15 −17

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 ?: ''
		@@ -26,18 +24,18 @@ def initOptions(Map args) {
		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)

+3 −3

Original line number	Diff line number	Diff line
		@@ -11,11 +11,11 @@ process DEEPTOOLS_PLOTHEATMAP {
		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::deeptools=3.5.0" : null)
		conda (params.enable_conda ? 'bioconda::deeptools=3.5.1' : null)
		if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
		container "https://depot.galaxyproject.org/singularity/deeptools:3.5.0--py_0"
		container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
		} else {
		container "quay.io/biocontainers/deeptools:3.5.0--py_0"
		container "quay.io/biocontainers/deeptools:3.5.1--py_0"
		}

		input: