Consensus peaks working (8d473267) · Commits · Chaos / Cutandrun

conf/flowswitch.config

+6 −1

Original line number	Diff line number	Diff line
		@@ -11,11 +11,15 @@ params {
		run_input_check = true
		run_cat_fastq = true
		run_trim_galore_fastqc = true

		run_alignment = true
		run_q_filter = false
		run_mark_dups = true
		run_remove_dups = true

		run_peak_calling = true
		run_consensus_all = false

		run_reporting = true
		run_deep_tools = true
		run_multiqc = true
		@@ -28,6 +32,7 @@ params {
		params.callers = params.peakcaller ? params.peakcaller.split(',').collect{ it.trim().toLowerCase() } : ['seacr']

		if(params.dedup_target_reads) { params.dedup_control_only = false }
		if(params.consensus_peak_mode == 'all') { params.run_consensus_all = true }

		if(params.minimum_alignment_q_score > 0) { params.run_q_filter = true }
		if(params.skip_removeduplicates \|\| !params.run_mark_dups) { params.run_remove_dups = false }

conf/modules.config

+74 −30

Original line number	Diff line number	Diff line
		@@ -496,44 +496,88 @@ if(params.run_peak_calling && 'macs2' in params.callers) {
		}
		}

		/*
		========================================================================================
		CONSENSUS PEAKS
		========================================================================================
		*/

		// //TODO: PEAK PLOTTING options - infact all reporting options - how t
		if(params.run_peak_calling) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:AWK_NAME_PEAK_BED' {
		ext.command = "'{OFS = \"\\t\"} {print \$0, FILENAME}'"
		ext.ext = "bed"
		publishDir = [
		enabled: false
		]
		}

		withName: '.:CONSENSUS_PEAKS:SORT\|.:CONSENSUS_PEAKS_ALL:SORT' {
		ext.args = "-k1,1 -k2,2n"
		ext.ext = "bed"
		publishDir = [
		enabled: false
		]
		}

		// /*
		// ========================================================================================
		// CONSENSUS PEAKS
		// ========================================================================================
		// */
		withName: '.:CONSENSUS_PEAKS:BEDTOOLS_MERGE\|.:CONSENSUS_PEAKS_ALL:BEDTOOLS_MERGE' {
		ext.args = " -c 2,3,4,5,6,7,7 -o collapse,collapse,collapse,collapse,collapse,collapse,count_distinct"
		ext.suffix = ".consensus.peaks"
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/05_consensus_peaks" },
		mode: 'copy',
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		}

		withName: '.:CONSENSUS_PEAKS:PLOT_CONSENSUS_PEAKS\|.:CONSENSUS_PEAKS_ALL:PLOT_CONSENSUS_PEAKS' {
		publishDir = [
		path: { "${params.outdir}/04_reporting" },
		mode: 'copy',
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: params.skip_upset_plots
		]
		}
		}
		}

		if(params.run_peak_calling && !params.run_consensus_all) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:CONSENSUS_PEAKS:AWK' {
		ext.command = "' \$10 >= 1 {print \$0}'"
		ext.ext = "bed"
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/05_consensus_peaks" },
		mode: 'copy',
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		}
		}
		}

		if(params.run_peak_calling && params.run_consensus_all) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:CONSENSUS_PEAKS_ALL:AWK' {
		ext.command = "' \$10 >= " + params.replicate_threshold.toString() + " {print \$0}'"
		ext.ext = "bed"
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/05_consensus_peaks" },
		mode: 'copy',
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		}
		}
		}

		// //TODO: PEAK PLOTTING options - infact all reporting options - how t

		// "awk_name_peak_bed" {
		// command = "'{OFS = \"\\t\"} {print \$0, FILENAME}'"
		// publish_files = false
		// ext = "bed"
		// }

		// "sort_group_peaks" {
		// args = "-k1,1 -k2,2n"
		// publish_files = false
		// ext = "bed"
		// }

		// "bedtools_merge_groups" {
		// args = " -c 2,3,4,5,6,7,7 -o collapse,collapse,collapse,collapse,collapse,collapse,count_distinct"
		// // args = " -c 7 -o collapse"
		// publish_dir = "03_peak_calling/05_consensus_peaks"
		// suffix = ".consensus.peaks"
		// }

		// "awk_threshold" {
		// publish_dir = "03_peak_calling/05_consensus_peaks"
		// suffix = ".consensus.peaks.filtered"
		// ext = "bed"
		// }

		// "plot_peaks" {
		// publish_dir = "04_reporting"
		// }

		// /*
		// ========================================================================================

modules/local/modules/plot_consensus_peaks/main.nf

+0 −4

Original line number	Diff line number	Diff line
		process PLOT_CONSENSUS_PEAKS {
		label 'process_low'
		publishDir "${params.outdir}",
		mode: params.publish_dir_mode,
		saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }


		conda (params.enable_conda ? "conda-forge::python=3.8.3 conda-forge::numpy=1.20.* conda-forge::pandas=1.2.* conda-forge::upsetplot=0.4.4" : null)
		container "luslab/cutandrun-dev-plot-consensus-peaks:latest"

nextflow.config

+4 −1

Original line number	Diff line number	Diff line
		@@ -73,12 +73,15 @@ params {
		macs2_gsize = 2.7e9
		run_narrow_peak = false

		// Consensus Peaks
		consensus_peak_mode = 'group'
		skip_upset_plots = false

		// Reporting and Visualisation
		skip_reporting = false
		skip_igv = false
		skip_heatmaps = false
		skip_multiqc = false
		skip_upset_plots = false

		// Boilerplate options
		outdir = "./results"

subworkflows/local/consensus_peaks.nf

+2 −4

Original line number	Diff line number	Diff line
		@@ -2,11 +2,10 @@
		* Create group consensus peaks
		*/


		include { SORT } from '../../modules/local/linux/sort'
		include { BEDTOOLS_MERGE } from '../../modules/nf-core/modules/bedtools/merge/main'
		include { AWK } from '../../modules/local/linux/awk'
		include { PLOT_CONSENSUS_PEAKS } from '../../modules/local/python/plot_consensus_peaks'
		include { PLOT_CONSENSUS_PEAKS } from '../../modules/local/modules/plot_consensus_peaks/main'

		workflow CONSENSUS_PEAKS {

		@@ -14,7 +13,6 @@ workflow CONSENSUS_PEAKS {
		bed // channel: [ val(meta), [ bed ], count]
		skip_plot // boolean: true/false


		main:
		ch_versions = Channel.empty()

		@@ -31,7 +29,7 @@ workflow CONSENSUS_PEAKS {

		// Plot consensus peak sets
		if(!skip_plot) {
		PLOT_CONSENSUS_PEAKS ( BEDTOOLS_MERGE.out.bed.collect{it[1]}.ifEmpty([]) )
		PLOT_CONSENSUS_PEAKS ( BEDTOOLS_MERGE.out.bed.collect{it[1]} )
		ch_versions = ch_versions.mix(PLOT_CONSENSUS_PEAKS.out.versions)
		}

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