Added peaking calling normalisation options (b8cfd2b0) · Commits · Chaos / Cutandrun

conf/modules.config

+28 −6

Original line number	Diff line number	Diff line
		@@ -440,15 +440,38 @@ if (params.run_mark_dups) {
		========================================================================================
		*/

		if(params.run_peak_calling) {
		if(params.run_peak_calling && (params.normalisation_mode == "Spikein" \|\| params.normalisation_mode == "None")) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:BEDTOOLS_GENOMECOV' {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:BEDTOOLS_GENOMECOV' {
		ext.args = "-bg"
		publishDir = [
		enabled: false
		]
		}
		}
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:BEDTOOLS_SORT' {
		if(params.run_peak_calling && (params.normalisation_mode != "Spikein" && params.normalisation_mode != "None")) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:DEEPTOOLS_BAMCOVERAGE' {
		ext.args = [
		'--outFileFormat bedgraph',
		'--skipNAs',
		"--binSize ${params.normalisation_binsize}",
		"--normalizeUsing ${params.normalisation_mode}"
		].join(' ').trim()
		ext.prefix = { "${meta.id}.bedgraph" }
		publishDir = [
		enabled: false
		]
		cache = false
		}
		}
		}

		if(params.run_peak_calling) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:BEDTOOLS_SORT' {
		ext.prefix = { "${meta.id}.sorted" }
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/01_bam_to_bedgraph" },
		@@ -458,7 +481,7 @@ if(params.run_peak_calling) {
		]
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:UCSC_BEDCLIP' {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:UCSC_BEDCLIP' {
		ext.prefix = { "${meta.id}.clipped" }
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/02_clip_bed" },
		@@ -468,7 +491,7 @@ if(params.run_peak_calling) {
		]
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:UCSC_BEDGRAPHTOBIGWIG' {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:UCSC_BEDGRAPHTOBIGWIG' {
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/03_bed_to_bigwig" },
		mode: 'copy',
		@@ -542,7 +565,6 @@ if(params.run_peak_calling) {
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		cache = false
		}

		withName: '.:CONSENSUS_PEAKS:PLOT_CONSENSUS_PEAKS\|.:CONSENSUS_PEAKS_ALL:PLOT_CONSENSUS_PEAKS' {

modules.json

+3 −0

Original line number	Diff line number	Diff line
		@@ -30,6 +30,9 @@
		"custom/getchromsizes": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		},
		"deeptools/bamcoverage": {
		"git_sha": "fdb1664885480d9411c24ba45bb4fde4738e5907"
		},
		"deeptools/computematrix": {
		"git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
		},

modules/nf-core/modules/deeptools/bamcoverage/main.nf

0 → 100644

+37 −0

Original line number	Diff line number	Diff line
		process DEEPTOOLS_BAMCOVERAGE {
		tag "$meta.id"
		label 'process_low'

		conda (params.enable_conda ? "bioconda::deeptools=3.5.1" : null)
		container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
		'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0':
		'quay.io/biocontainers/deeptools:3.5.1--py_0' }"

		input:
		tuple val(meta), path(input), path(input_index)

		output:
		tuple val(meta), path("*.bigWig") , emit: bigwig, optional: true
		tuple val(meta), path("*.bedgraph") , emit: bedgraph, optional: true
		path "versions.yml" , emit: versions

		when:
		task.ext.when == null \|\| task.ext.when

		script:
		def args = task.ext.args ?: ''
		def prefix = task.ext.prefix ?: "${meta.id}.bigWig"

		"""
		bamCoverage \
		--bam $input \
		$args \
		--numberOfProcessors ${task.cpus} \
		--outFileName ${prefix}

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

modules/nf-core/modules/deeptools/bamcoverage/meta.yml

0 → 100644

+49 −0

Original line number	Diff line number	Diff line
		name: deeptools_bamcoverage
		description: This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output.
		keywords:
		- sort
		tools:
		- deeptools:
		description: A set of user-friendly tools for normalization and visualzation of deep-sequencing data
		homepage: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
		documentation: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html
		tool_dev_url: https://github.com/deeptools/deepTools/
		doi: "https://doi.org/10.1093/nar/gkw257"
		licence: ['GPL v3']

		input:
		- meta:
		type: map
		description: \|
		Groovy Map containing sample information
		e.g. [ id:'test', single_end:false ]
		- input:
		type: file
		description: BAM/CRAM file
		pattern: "*.{bam,cram}"
		- input_index:
		type: file
		description: BAM/CRAM index file
		pattern: "*.{bai,crai}"

		output:
		- meta:
		type: map
		description: \|
		Groovy Map containing sample information
		e.g. [ id:'test', single_end:false ]
		- versions:
		type: file
		description: File containing software versions
		pattern: "versions.yml"
		- bigWig:
		type: file
		description: BigWig file
		pattern: "*.bigWig"
		- bedgraph:
		type: file
		description: Bedgraph file
		pattern: "*.bedgraph"

		authors:
		- "@FriederikeHanssen"

nextflow.config

+2 −1

Original line number	Diff line number	Diff line
		@@ -57,7 +57,8 @@ params {
		only_filtering = false

		// Read Normalisation
		skip_scale = false
		normalisation_mode = "Spikein"
		normalisation_binsize = 1
		normalisation_c = 10000

		// Peak Caller default param

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