Updated the seacr module (ae2eb1e8) · Commits · Chaos / Cutandrun

modules.json

+1 −1

Original line number	Diff line number	Diff line
		@@ -55,7 +55,7 @@
		"git_sha": "c5235a983d454787fa0c3247b02086969217163b"
		},
		"seacr/callpeak": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		"git_sha": "4d89d6b2f0c478ac7ef80ece5cad44fdf7ffd614"
		},
		"ucsc/bedclip": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"

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

+32 −22

Original line number	Diff line number	Diff line
		@@ -9,6 +9,13 @@ 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
		//
		@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
		// 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 ]

		// Do not publish versions.yml unless running from pytest workflow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) {
		@@ -65,4 +76,3 @@ def saveFiles(Map args) {
		return "${getPathFromList(path_list)}/$args.filename"
		}
		}
		}

modules/nf-core/modules/seacr/callpeak/main.nf

+15 −10

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

		params.options = [:]
		options = initOptions(params.options)
		@@ -13,30 +13,35 @@ process SEACR_CALLPEAK {
		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::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.29.2" : null)
		conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null)
		if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
		container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0"
		container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0"
		} else {
		container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0'
		container 'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0'
		}

		input:
		tuple val(meta), path(bedgraph), path(ctrlbedgraph)
		val (threshold)

		output:
		tuple val(meta), path("*.bed"), emit: bed
		path "*.version.txt" , emit: version
		path "versions.yml" , emit: versions

		script:
		def software = getSoftwareName(task.process)
		def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
		def function_switch = ctrlbedgraph ? "$ctrlbedgraph" : "$threshold"
		"""
		SEACR_1.3.sh \\
		$bedgraph \\
		$ctrlbedgraph \\
		$function_switch \\
		$options.args \\
		$prefix

		echo $VERSION > ${software}.version.txt
		cat <<-END_VERSIONS > versions.yml
		${getProcessName(task.process)}:
		${getSoftwareName(task.process)}: \$(echo $VERSION)
		bedtools: \$(bedtools --version \| sed -e "s/bedtools v//g")
		r-base: \$(echo \$(R --version 2>&1) \| sed 's/^.R version //; s/ .\$//')
		END_VERSIONS
		"""
		}

modules/nf-core/modules/seacr/callpeak/meta.yml

+8 −3

Original line number	Diff line number	Diff line

		name: seacr_callpeak
		description: Call peaks using SEACR on sequenced reads in bedgraph format
		keywords:
		@@ -30,6 +31,10 @@ input:
		type: file
		description: \|
		Control (IgG) data bedgraph file to generate an empirical threshold for peak calling.
		- threshold:
		type: value
		description: \|
		Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph
		output:
		- meta:
		type: map
		@@ -40,9 +45,9 @@ output:
		type: file
		description: Bed file containing the calculated peaks.
		pattern: "*.bed"
		- version:
		- versions:
		type: file
		description: File containing software version
		pattern: "*.{version.txt}"
		description: File containing software versions
		pattern: "versions.yml"
		authors:
		- "@chris-cheshire"

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