Merge branch 'peakcallers' into dev (2f944afd) · Commits · Chaos / Cutandrun

.github/workflows/ci.yml

+16 −1

Original line number	Diff line number	Diff line
		@@ -145,7 +145,22 @@ jobs:
		fail-fast: false
		matrix:
		nxf_version: ['21.10.3', '']
		tags: ["samplesheet", "verify_output_input", "verify_output_align_short", "verify_output_align_long", "verify_output_peak_calling", "verify_output_reporting", "verify_output_save", "verify_output_skip"]
		tags:
		- samplesheet
		- verify_output_input
		- verify_output_peak_calling
		- verify_output_reporting
		- verify_output_save
		- verify_output_skip
		- verify_output_align_only_q_filter
		- verify_output_align_duplicates_mark
		- verify_output_align_duplicates_remove
		- verify_output_align_duplicates_remove_target
		- verify_output_align_intermed
		- verify_output_align_only_align
		- verify_output_align_save_spikein_align
		- verify_output_align_save_unaligned
		- test_peak_callers
		steps:
		- uses: actions/checkout@v2

conf/modules.config

+7 −1

Original line number	Diff line number	Diff line
		@@ -161,7 +161,13 @@ params {

		"seacr" {
		args = "non stringent"
		suffix = ".peaks.bed"
		suffix = ".seacr.peaks.bed"
		publish_dir = "03_peak_calling/04_called_peaks"
		}

		"macs2" {
		args = ""
		suffix = ".macs2.peaks.bed"
		publish_dir = "03_peak_calling/04_called_peaks"
		}

modules.json

+3 −0

Original line number	Diff line number	Diff line
		@@ -42,6 +42,9 @@
		"gunzip": {
		"git_sha": "e560fbbc3ed68e62bc810a50f552394056f81762"
		},
		"macs2/callpeak": {
		"git_sha": "20d8250d9f39ddb05dfb437603aaf99b5c0b2b41"
		},
		"picard/markduplicates": {
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},

modules/local/modules/generate_reports/main.nf

+1 −1

Original line number	Diff line number	Diff line
		@@ -35,7 +35,7 @@ process GENERATE_REPORTS {
		--meta_ctrl $meta_data_ctrl \\
		--raw_frag "*.frag_len.txt" \\
		--bin_frag "*bin500.awk.bed" \\
		--seacr_bed "bed..bed" \\
		--seacr_bed "bed.bed" \\
		--output . \\
		--log log.txt

modules/nf-core/modules/macs2/callpeak/functions.nf

0 → 100644

+78 −0

Original line number	Diff line number	Diff line
		//
		// 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"
		}
		}
		No newline at end of file

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