Merge branch 'chris_feat' into dev (886f9527) · Commits · Chaos / Cutandrun

bin/peak_reproducability.py

+2 −2

Original line number	Diff line number	Diff line
		@@ -35,7 +35,7 @@ peak_perc = 0
		print('Reading file')

		# Read file in using dask
		ddf_inter = dd.read_csv(args.intersect, sep='\t', header=None, names=['chrom','start','end','overlap_1','key','a_name','b_name','count'])
		ddf_inter = dd.read_csv(args.intersect, sep='\t', header=None, names=['chrom','start','end','overlap_1','key','a_name','b_name','count'], dtype={'overlap_1': 'float64'})

		# Find number of files
		numfiles = ddf_inter['b_name'].max().compute()
		@@ -44,7 +44,7 @@ numfiles = ddf_inter['b_name'].max().compute()
		if isinstance(numfiles, str):
		print('Detected single file, reloading table')
		numfiles = 1
		ddf_inter = dd.read_csv(args.intersect, sep='\t', header=None, names=['chrom','start','end','overlap_1','overlap_2','key','name','count'])
		ddf_inter = dd.read_csv(args.intersect, sep='\t', header=None, names=['chrom','start','end','overlap_1','overlap_2','key','name','count'], dtype={'overlap_1': 'float64', 'overlap_2': 'float64'})

		print('Number of files: ' + str(numfiles))

conf/modules.config

+6 −0

Original line number	Diff line number	Diff line
		@@ -141,7 +141,13 @@ params {
		*/

		"bedtools_genomecov_bedgraph" {
		//publish_dir = "03_peak_calling/01_bam_to_bedgraph"
		publish_files = false
		}

		"sort_bedgraph" {
		publish_dir = "03_peak_calling/01_bam_to_bedgraph"
		suffix = ".sorted"
		}

		"ucsc_bedclip" {

modules.json

+6 −0

Original line number	Diff line number	Diff line
		@@ -6,12 +6,18 @@
		"bedtools/bamtobed": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		},
		"bedtools/genomecov": {
		"git_sha": "e8b33e6eb1be2a03abdd2c06068f9a5cebc02bb4"
		},
		"bedtools/intersect": {
		"git_sha": "49da8642876ae4d91128168cd0db4f1c858d7792"
		},
		"bedtools/merge": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		},
		"bedtools/sort": {
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"bowtie2/align": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		},

modules/nf-core/modules/bedtools/genomecov/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"
		}
		}

modules/nf-core/modules/bedtools/genomecov/main.nf

0 → 100644

+68 −0

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

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

		process BEDTOOLS_GENOMECOV {
		tag "$meta.id"
		label 'process_medium'
		publishDir "${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::bedtools=2.30.0" : null)
		if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
		container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
		} else {
		container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
		}

		input:
		tuple val(meta), path(intervals), val(scale)
		path sizes
		val extension

		output:
		tuple val(meta), path("*.${extension}"), emit: genomecov
		path "versions.yml" , emit: versions

		script:
		def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
		def args_token = options.args.tokenize()
		def args = options.args
		args += (scale > 0 && scale != 1) ? " -scale $scale" : ""

		if (!args_token.contains('-bg') && (scale > 0 && scale != 1)) {
		args += " -bg"
		}

		if (intervals.name =~ /\.bam/) {
		"""
		bedtools \\
		genomecov \\
		-ibam $intervals \\
		$args \\
		> ${prefix}.${extension}

		cat <<-END_VERSIONS > versions.yml
		${getProcessName(task.process)}:
		${getSoftwareName(task.process)}: \$(bedtools --version \| sed -e "s/bedtools v//g")
		END_VERSIONS
		"""
		} else {
		"""
		bedtools \\
		genomecov \\
		-i $intervals \\
		-g $sizes \\
		$args \\
		> ${prefix}.${extension}

		cat <<-END_VERSIONS > versions.yml
		${getProcessName(task.process)}:
		${getSoftwareName(task.process)}: \$(bedtools --version \| sed -e "s/bedtools v//g")
		END_VERSIONS
		"""
		}
		}

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