Merge branch 'module_version_2' into dev (6eeba927) · Commits · Chaos / Cutandrun

assets/multiqc_config.yaml

+6 −0

Original line number	Diff line number	Diff line
		@@ -46,6 +46,12 @@ module_order:
		- picard
		- custom_content

		custom_content:
		order:
		- fragment_lengths
		- software_versions
		- software_versions_unique

		# Don't show % Dups in the General Stats table (we have this from Picard)
		table_columns_visible:
		FastQC:

conf/modules.config

+2 −2

Original line number	Diff line number	Diff line
		@@ -91,7 +91,7 @@ params {
		*/

		"picard_markduplicates" {
		args = "ASSUME_SORTED=true REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp"
		args = "-ASSUME_SORT_ORDER coordinate -REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT -TMP_DIR tmp"
		suffix = ".target.markdup"
		publish_files = false
		}
		@@ -101,7 +101,7 @@ params {
		}

		"picard_dedup" {
		args = "ASSUME_SORTED=true REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp"
		args = "-ASSUME_SORT_ORDER coordinate -REMOVE_DUPLICATES true -VALIDATION_STRINGENCY LENIENT -TMP_DIR tmp"
		suffix = ".target.dedup"
		publish_files = false
		}

modules.json

+19 −22

Original line number	Diff line number	Diff line
		@@ -4,7 +4,7 @@
		"repos": {
		"nf-core/modules": {
		"bedtools/bamtobed": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"bedtools/genomecov": {
		"git_sha": "e8b33e6eb1be2a03abdd2c06068f9a5cebc02bb4"
		@@ -13,64 +13,61 @@
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"bedtools/merge": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"bedtools/sort": {
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		"git_sha": "2959b4ba070d138d1577acc48d35cc669fbef972"
		},
		"bowtie2/align": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"bowtie2/build": {
		"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"cat/fastq": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"deeptools/computematrix": {
		"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"deeptools/plotheatmap": {
		"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"fastqc": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		},
		"gunzip": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"picard/markduplicates": {
		"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"samtools/flagstat": {
		"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"samtools/idxstats": {
		"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"samtools/index": {
		"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"samtools/sort": {
		"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"samtools/stats": {
		"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"samtools/view": {
		"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"seacr/callpeak": {
		"git_sha": "4d89d6b2f0c478ac7ef80ece5cad44fdf7ffd614"
		},
		"ucsc/bedclip": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"ucsc/bedgraphtobigwig": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"untar": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		}
		}
		}

modules/local/common/functions.nf

+59 −39

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
		*/
		//
		// 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.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)

		// 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) {
		@@ -56,4 +76,4 @@ def saveFiles(Map args) {
		return "${getPathFromList(path_list)}/$args.filename"
		}
		}
		}

modules/local/export_meta.nf

+1 −1

Original line number	Diff line number	Diff line
		include { initOptions; saveFiles; getSoftwareName } from './common/functions'
		include { initOptions; saveFiles; getSoftwareName; getProcessName } from './common/functions'

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

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