Peak calling working (057cef16) · Commits · Chaos / Cutandrun

conf/flowswitch.config

+3 −0

Original line number	Diff line number	Diff line
		@@ -5,6 +5,7 @@
		* ---------------------------------------------------
		*/

		// Defaults
		params {
		run_genome_prep = true
		run_input_check = true
		@@ -24,6 +25,8 @@ params {
		dedup_control_only = true
		}

		params.callers = params.peakcaller ? params.peakcaller.split(',').collect{ it.trim().toLowerCase() } : ['seacr']

		if(params.dedup_target_reads) { params.dedup_control_only = false }

		if(params.minimum_alignment_q_score > 0) { params.run_q_filter = true }

conf/modules.config

+28 −37

Original line number	Diff line number	Diff line
		@@ -466,49 +466,40 @@ if(params.run_peak_calling) {
		}
		}

		// "seacr" {
		// args = "non stringent"
		// suffix = ".seacr.peaks.bed"
		// publish_dir = "03_peak_calling/04_called_peaks"
		// }

		// "macs2" {
		// args = ""
		// suffix = ".macs2.peaks.bed"
		// publish_dir = "03_peak_calling/04_called_peaks"
		// }











		if(params.run_peak_calling && 'seacr' in params.callers) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:SEACR_.*' {
		ext.args = "non stringent"
		ext.prefix = { "${meta.id}.seacr.peaks.bed" }
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/04_called_peaks" },
		mode: 'copy',
		pattern: "*.bed",
		enabled: true
		]
		}
		}
		}

		if(params.run_peak_calling && 'macs2' in params.callers) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:MACS2_.*' {
		ext.args = "-p ${params.macs2_pvalue}"
		ext.prefix = { "${meta.id}.macs2.peaks.bed" }
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/04_called_peaks" },
		mode: 'copy',
		pattern: "*.bed",
		enabled: true
		]
		}
		}
		}


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

















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

workflows/cutandrun.nf

+78 −91

Original line number	Diff line number	Diff line
		@@ -70,11 +70,6 @@ ch_frag_len_header_multiqc = file("$projectDir/assets/multiqc/frag_len_header.tx
		// Init
		def prepare_tool_indices = ["bowtie2"]

		// // Peak caller options
		// macs2_callpeak_options = modules["macs2"]
		// macs2_callpeak_options.args = macs2_callpeak_options.args + " -p " + params.macs_pvalue

		// Check peakcaller options
		caller_list = ['seacr', 'macs2']
		callers = params.peakcaller ? params.peakcaller.split(',').collect{ it.trim().toLowerCase() } : ['seacr']
		if ((caller_list + callers).unique().size() != caller_list.size()) {
		@@ -152,10 +147,10 @@ include { BEDTOOLS_GENOMECOV } from "../mo
		include { BEDTOOLS_SORT } from "../modules/nf-core/modules/bedtools/sort/main"
		include { UCSC_BEDCLIP } from "../modules/nf-core/modules/ucsc/bedclip/main"
		include { UCSC_BEDGRAPHTOBIGWIG } from "../modules/nf-core/modules/ucsc/bedgraphtobigwig/main"
		// include { SEACR_CALLPEAK } from "../modules/nf-core/modules/seacr/callpeak/main" addParams( options: modules["seacr"] )
		// include { SEACR_CALLPEAK as SEACR_CALLPEAK_NOIGG } from "../modules/nf-core/modules/seacr/callpeak/main" addParams( options: modules["seacr"] )
		// include { MACS2_CALLPEAK } from "../modules/nf-core/modules/macs2/callpeak/main" addParams( options: macs2_callpeak_options )
		// include { MACS2_CALLPEAK as MACS2_CALLPEAK_NOIGG } from "../modules/nf-core/modules/macs2/callpeak/main" addParams( options: macs2_callpeak_options )
		include { SEACR_CALLPEAK } from "../modules/nf-core/modules/seacr/callpeak/main"
		include { SEACR_CALLPEAK as SEACR_CALLPEAK_NOIGG } from "../modules/nf-core/modules/seacr/callpeak/main"
		include { MACS2_CALLPEAK } from "../modules/nf-core/modules/macs2/callpeak/main"
		include { MACS2_CALLPEAK as MACS2_CALLPEAK_NOIGG } from "../modules/nf-core/modules/macs2/callpeak/main"
		// include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_GENE } from "../modules/nf-core/modules/deeptools/computematrix/main" addParams( options: modules["dt_compute_mat_gene"] )
		// include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_PEAKS } from "../modules/nf-core/modules/deeptools/computematrix/main" addParams( options: modules["dt_compute_mat_peaks"] )
		// include { DEEPTOOLS_PLOTHEATMAP as DEEPTOOLS_PLOTHEATMAP_GENE } from "../modules/nf-core/modules/deeptools/plotheatmap/main" addParams( options: modules["dt_plotheatmap_gene"] )
		@@ -514,83 +509,79 @@ workflow CUTANDRUN {
		/*
		* CHANNEL: Pull control groups
		*/
		// ch_bedgraph_split.target.map{
		// row -> [row[0].control_group, row]
		// }
		// .set { ch_bg_target_ctrlgrp }
		ch_bedgraph_split.target.map{
		row -> [row[0].control_group, row]
		}
		.set { ch_bg_target_ctrlgrp }
		//ch_bg_target_ctrlgrp \| view

		// ch_bedgraph_split.control.map{
		// row -> [row[0].control_group, row]
		// }
		// .set { ch_bg_control_ctrlgrp }
		ch_bedgraph_split.control.map{
		row -> [row[0].control_group, row]
		}
		.set { ch_bg_control_ctrlgrp }
		//ch_bg_control_ctrlgrp \| view

		/*
		* CHANNEL: Create target/control pairings
		*/
		// Create pairs of controls (IgG) with target samples if they are supplied
		// ch_bg_control_ctrlgrp.cross(ch_bg_target_ctrlgrp)
		// .map {
		// row -> [row[1][1][0], row[1][1][1], row[0][1][1]]
		// }
		// .set{ ch_bedgraph_paired }
		ch_bg_control_ctrlgrp.cross(ch_bg_target_ctrlgrp).map {
		row -> [row[1][1][0], row[1][1][1], row[0][1][1]]
		}
		.set{ ch_bedgraph_paired }
		// EXAMPLE CHANNEL STRUCT: [[META], TARGET_BEDGRAPH, CONTROL_BEDGRAPH]
		//ch_bedgraph_paired \| view

		// SEACR_CALLPEAK (
		// ch_bedgraph_paired,
		// params.peak_threshold
		// )
		// ch_seacr_bed = SEACR_CALLPEAK.out.bed
		// ch_software_versions = ch_software_versions.mix(SEACR_CALLPEAK.out.versions)
		//ch_software_versions = ch_software_versions.mix(SEACR_CALLPEAK.out.versions)
		SEACR_CALLPEAK (
		ch_bedgraph_paired,
		params.peak_threshold
		)
		ch_seacr_bed = SEACR_CALLPEAK.out.bed
		ch_software_versions = ch_software_versions.mix(SEACR_CALLPEAK.out.versions)
		// EXAMPLE CHANNEL STRUCT: [[META], BED]
		//SEACR_CALLPEAK.out.bed \| view
		}

		if('macs2' in callers) {
		// ch_samtools_bam
		// .branch{ it ->
		// target: it[0].group != "igg"
		// control: it[0].group == "igg"
		// }
		// .set { ch_samtools_bam_split }
		ch_samtools_bam.branch{ it ->
		target: it[0].group != "igg"
		control: it[0].group == "igg"
		}
		.set { ch_samtools_bam_split }
		// ch_samtools_bam_split.target \| view

		/*
		* CHANNEL: Pull control groups
		*/
		// ch_samtools_bam_split.target.map{
		// row -> [row[0].control_group, row]
		// }
		// .set { ch_bam_target_ctrlgrp }
		// //ch_bam_target_ctrlgrp \| view
		ch_samtools_bam_split.target.map{
		row -> [row[0].control_group, row]
		}
		.set { ch_bam_target_ctrlgrp }
		//ch_bam_target_ctrlgrp \| view

		// ch_samtools_bam_split.control.map{
		// row -> [row[0].control_group, row]
		// }
		// .set { ch_bam_control_ctrlgrp }
		ch_samtools_bam_split.control.map{
		row -> [row[0].control_group, row]
		}
		.set { ch_bam_control_ctrlgrp }
		// ch_bam_control_ctrlgrp \| view

		/*
		* CHANNEL: Create target/control pairings
		*/
		// Create pairs of controls (IgG) with target samples if they are supplied
		// ch_bam_control_ctrlgrp.cross(ch_bam_target_ctrlgrp)
		// .map{
		// row -> [row[1][1][0], row[1][1][1], row[0][1][1]]
		// }
		// .set{ch_bam_paired}
		ch_bam_control_ctrlgrp.cross(ch_bam_target_ctrlgrp).map{
		row -> [row[1][1][0], row[1][1][1], row[0][1][1]]
		}
		.set{ch_bam_paired}
		// EXAMPLE CHANNEL STRUCT: [[META], TARGET_BAM, CONTROL_BAM]
		// ch_bam_paired \| view

		// MACS2_CALLPEAK (
		// ch_bam_paired,
		// params.macs2_gsize
		// )
		// ch_macs2_bed = MACS2_CALLPEAK.out.bed
		// ch_software_versions = ch_software_versions.mix(MACS2_CALLPEAK.out.versions)
		MACS2_CALLPEAK (
		ch_bam_paired,
		params.macs2_gsize
		)
		ch_macs2_bed = MACS2_CALLPEAK.out.bed
		ch_software_versions = ch_software_versions.mix(MACS2_CALLPEAK.out.versions)
		// EXAMPLE CHANNEL STRUCT: [[META], BED]
		//MACS2_CALLPEAK.out.bed \| view
		}
		@@ -603,52 +594,48 @@ workflow CUTANDRUN {
		/*
		* CHANNEL: Add fake control channel
		*/
		// ch_bedgraph_split.target
		// .map{ row-> [ row[0], row[1], [] ] }
		// .set { ch_bedgraph_target_fctrl }
		ch_bedgraph_split.target.map{ row-> [ row[0], row[1], [] ] }
		.set { ch_bedgraph_target_fctrl }
		// EXAMPLE CHANNEL STRUCT: [[META], BED, FAKE_CTRL]
		// ch_bedgraph_target_fctrl \| view

		// SEACR_CALLPEAK_NOIGG (
		// ch_bedgraph_target_fctrl,
		// params.peak_threshold
		// )
		// ch_seacr_bed = SEACR_CALLPEAK_NOIGG.out.bed
		// ch_software_versions = ch_software_versions.mix(SEACR_CALLPEAK_NOIGG.out.versions)
		//ch_software_versions = ch_software_versions.mix(SEACR_NO_IGG.out.versions)
		SEACR_CALLPEAK_NOIGG (
		ch_bedgraph_target_fctrl,
		params.peak_threshold
		)
		ch_seacr_bed = SEACR_CALLPEAK_NOIGG.out.bed
		ch_software_versions = ch_software_versions.mix(SEACR_CALLPEAK_NOIGG.out.versions)
		// EXAMPLE CHANNEL STRUCT: [[META], BED]
		//SEACR_NO_IGG.out.bed \| view
		}

		if('macs2' in callers) {
		// ch_samtools_bam
		// .branch{ it ->
		// target: it[0].group != "igg"
		// control: it[0].group == "igg"
		// }
		// .set { ch_samtools_bam_split }
		// // ch_samtools_bam_split.target \| view

		// /*
		// * CHANNEL: Add fake control channel
		// */
		// ch_samtools_bam_split.target
		// .map{ row-> [ row[0], row[1], [] ] }
		// .set { ch_samtools_bam_target_fctrl }
		// // EXAMPLE CHANNEL STRUCT: [[META], BAM, FAKE_CTRL]
		// //ch_samtools_bam_target_fctrl \| view

		// MACS2_CALLPEAK_NOIGG (
		// ch_samtools_bam_target_fctrl,
		// params.macs2_gsize
		// )
		// ch_macs2_bed = MACS2_CALLPEAK_NOIGG.out.bed
		// ch_software_versions = ch_software_versions.mix(MACS2_CALLPEAK_NOIGG.out.versions)
		//ch_software_versions = ch_software_versions.mix(MACS2_CALLPEAK_NOIGG.out.versions)
		ch_samtools_bam.branch{ it ->
		target: it[0].group != "igg"
		control: it[0].group == "igg"
		}
		.set { ch_samtools_bam_split }
		// ch_samtools_bam_split.target \| view

		/*
		* CHANNEL: Add fake control channel
		*/
		ch_samtools_bam_split.target.map{ row-> [ row[0], row[1], [] ] }
		.set { ch_samtools_bam_target_fctrl }
		// EXAMPLE CHANNEL STRUCT: [[META], BAM, FAKE_CTRL]
		//ch_samtools_bam_target_fctrl \| view

		MACS2_CALLPEAK_NOIGG (
		ch_samtools_bam_target_fctrl,
		params.macs2_gsize
		)
		ch_macs2_bed = MACS2_CALLPEAK_NOIGG.out.bed
		ch_software_versions = ch_software_versions.mix(MACS2_CALLPEAK_NOIGG.out.versions)
		// EXAMPLE CHANNEL STRUCT: [[META], BED]
		// MACS2_CALLPEAK_NOIGG.out.bed \| view
		}
		}

		// Store output of primary peakcaller in the output channel
		// if(callers[0] == 'seacr') {
		// ch_peaks_bed = ch_seacr_bed

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