igv and deep tools working (ad0dac1c) · Commits · Chaos / Cutandrun

conf/modules.config

+64 −35

Original line number	Diff line number	Diff line
		@@ -652,48 +652,77 @@ if(params.run_peak_calling) {
		}
		}

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





		/*
		========================================================================================
		REPORTING
		========================================================================================
		*/

		// /*
		// ========================================================================================
		// REPORTING
		// ========================================================================================
		// */
		if(params.run_reporting && params.run_igv) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:IGV_SESSION' {
		publishDir = [
		path: { "${params.outdir}/04_reporting/igv" },
		mode: 'copy',
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		}
		}
		}

		// "igv" {
		// publish_dir = "04_reporting/igv"
		// }
		if(params.run_reporting && params.run_deep_tools) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:AWK_EDIT_PEAK_BED' {
		ext.command = "'{split(\$6, summit, \":\"); split(summit[2], region, \"-\"); print summit[1]\"\\t\"region[1]\"\\t\"region[2]}'"
		ext.suffix = ".max_signal"
		publishDir = [
		enabled: false
		]
		}

		// "dt_compute_mat_gene" {
		// args = "scale-regions --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros --missingDataAsZero"
		// publish_dir = "04_reporting/heatmaps/gene"
		// }
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_COMPUTEMATRIX_GENE' {
		ext.args = "scale-regions --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros --missingDataAsZero"
		publishDir = [
		path: { "${params.outdir}/04_reporting/heatmaps/gene" },
		mode: 'copy',
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		}

		// "dt_compute_mat_peaks" {
		// args = "reference-point -a 3000 -b 3000 --referencePoint center --skipZeros --missingDataAsZero"
		// publish_dir = "04_reporting/heatmaps/peaks"
		// }
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_PLOTHEATMAP_GENE' {
		ext.args = "--sortUsing sum"
		publishDir = [
		path: { "${params.outdir}/04_reporting/heatmaps/gene" },
		mode: 'copy',
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		}

		// "dt_plotheatmap_gene" {
		// args = "--sortUsing sum"
		// publish_dir = "04_reporting/heatmaps/gene"
		// }
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_COMPUTEMATRIX_PEAKS' {
		ext.args = "reference-point -a 3000 -b 3000 --referencePoint center --skipZeros --missingDataAsZero"
		publishDir = [
		path: { "${params.outdir}/04_reporting/heatmaps/peaks" },
		mode: 'copy',
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		}

		// "dt_plotheatmap_peaks" {
		// args = "--sortUsing sum --startLabel \"Peak Start\" --endLabel \"Peak End\" --xAxisLabel \"\" --regionsLabel \"Peaks\""
		// publish_dir = "04_reporting/heatmaps/peaks"
		// }
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_PLOTHEATMAP_PEAKS' {
		ext.args = "--sortUsing sum --startLabel \"Peak Start\" --endLabel \"Peak End\" --xAxisLabel \"\" --regionsLabel \"Peaks\""
		publishDir = [
		path: { "${params.outdir}/04_reporting/heatmaps/peaks" },
		mode: 'copy',
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		}
		}
		}

		// "awk_edit_peak_bed" {
		// command = "'{split(\$6, summit, \":\"); split(summit[2], region, \"-\"); print summit[1]\"\\t\"region[1]\"\\t\"region[2]}'"
		// suffix = ".max_signal"
		// publish_files = false
		// }

		// "export_meta" {
		// publish_dir = "04_reporting"

modules/local/python/igv_session.nf

+0 −3

Original line number	Diff line number	Diff line
		@@ -3,9 +3,6 @@ colour_pallete = ['38,70,83', '231,111,81', '42,157,143', '244,162,97', '233,196
		process IGV_SESSION {
		tag "igv"
		label 'process_low'
		publishDir "${params.outdir}",
		mode: params.publish_dir_mode,
		saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'pipeline_info', publish_id:'') }

		conda (params.enable_conda ? "conda-forge::python=3.8.3" : null)
		container "quay.io/biocontainers/python:3.8.3"

workflows/cutandrun.nf

+53 −52

Original line number	Diff line number	Diff line
		@@ -102,8 +102,8 @@ include { INPUT_CHECK } from "../subworkflows/local/input_ch
		include { AWK as AWK_NAME_PEAK_BED } from "../modules/local/linux/awk"
		include { AWK as AWK_FRAG_BIN } from "../modules/local/linux/awk"
		include { SAMTOOLS_CUSTOMVIEW } from "../modules/local/samtools_custom_view"
		// include { IGV_SESSION } from "../modules/local/python/igv_session" addParams( options: modules["igv"] )
		// include { AWK as AWK_EDIT_PEAK_BED } from "../modules/local/linux/awk" addParams( options: modules["awk_edit_peak_bed"] )
		include { IGV_SESSION } from "../modules/local/python/igv_session"
		include { AWK as AWK_EDIT_PEAK_BED } from "../modules/local/linux/awk"
		// include { CALCULATE_FRIP } from "../modules/local/modules/calculate_frip/main" addParams( options: modules["calc_frip"] )
		// include { CUT as CUT_CALC_REPROD } from "../modules/local/linux/cut" addParams( options: modules["calc_peak_repro_cut"] )
		// include { CALCULATE_PEAK_REPROD } from "../modules/local/modules/calculate_peak_reprod/main" addParams( options: modules["calc_peak_repro"] )
		@@ -145,10 +145,10 @@ include { SEACR_CALLPEAK } from "../mo
		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"] )
		// include { DEEPTOOLS_PLOTHEATMAP as DEEPTOOLS_PLOTHEATMAP_PEAKS } from "../modules/nf-core/modules/deeptools/plotheatmap/main" addParams( options: modules["dt_plotheatmap_peaks"] )
		include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_GENE } from "../modules/nf-core/modules/deeptools/computematrix/main"
		include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_PEAKS } from "../modules/nf-core/modules/deeptools/computematrix/main"
		include { DEEPTOOLS_PLOTHEATMAP as DEEPTOOLS_PLOTHEATMAP_GENE } from "../modules/nf-core/modules/deeptools/plotheatmap/main"
		include { DEEPTOOLS_PLOTHEATMAP as DEEPTOOLS_PLOTHEATMAP_PEAKS } from "../modules/nf-core/modules/deeptools/plotheatmap/main"
		// include { BEDTOOLS_INTERSECT } from "../modules/nf-core/modules/bedtools/intersect/main.nf" addParams( options: bedtools_intersect_options )
		include { CUSTOM_DUMPSOFTWAREVERSIONS } from "../modules/local/modules/custom/dumpsoftwareversions/main"

		@@ -768,21 +768,20 @@ workflow CUTANDRUN {
		/*
		* CHANNEL: Remove IgG from bigwig channel
		*/
		// UCSC_BEDGRAPHTOBIGWIG.out.bigwig
		// .filter { it[0].group != "igg" }
		// .set { ch_bigwig_no_igg }
		UCSC_BEDGRAPHTOBIGWIG.out.bigwig
		.filter { it[0].group != "igg" }
		.set { ch_bigwig_no_igg }
		//ch_bigwig_no_igg \| view

		/*
		* MODULE: Create igv session
		*/
		// IGV_SESSION (
		// PREPARE_GENOME.out.fasta,
		// PREPARE_GENOME.out.gtf,
		// ch_peaks_bed.collect{it[1]}.ifEmpty([]),
		// UCSC_BEDGRAPHTOBIGWIG.out.bigwig.collect{it[1]}.ifEmpty([])
		// )
		//TODO - this version ouptut causes an error for an unknown reason
		IGV_SESSION (
		PREPARE_GENOME.out.fasta,
		PREPARE_GENOME.out.gtf,
		ch_peaks_bed.collect{it[1]}.ifEmpty([]),
		UCSC_BEDGRAPHTOBIGWIG.out.bigwig.collect{it[1]}.ifEmpty([])
		)
		//ch_software_versions = ch_software_versions.mix(IGV_SESSION.out.versions)
		}

		@@ -790,76 +789,78 @@ workflow CUTANDRUN {
		/*
		* MODULE: Extract max signal from peak beds
		*/
		// AWK_EDIT_PEAK_BED (
		// ch_peaks_bed
		// )
		// ch_software_versions = ch_software_versions.mix(AWK_EDIT_PEAK_BED.out.versions)
		AWK_EDIT_PEAK_BED (
		ch_peaks_bed
		)
		ch_software_versions = ch_software_versions.mix(AWK_EDIT_PEAK_BED.out.versions)
		//AWK_EDIT_PEAK_BED.out.file \| view

		/*
		* CHANNEL: Structure output for join on id
		*/
		// AWK_EDIT_PEAK_BED.out.file
		// .map { row -> [row[0].id, row ].flatten()}
		// .set { ch_peaks_bed_id }
		AWK_EDIT_PEAK_BED.out.file
		.map { row -> [row[0].id, row ].flatten()}
		.set { ch_peaks_bed_id }
		//ch_peaks_bed_id \| view

		/*
		* CHANNEL: Join beds and bigwigs on id
		*/
		// ch_bigwig_no_igg
		// .map { row -> [row[0].id, row ].flatten()}
		// .join ( ch_peaks_bed_id )
		// .set { ch_dt_peaks }
		ch_bigwig_no_igg
		.map { row -> [row[0].id, row ].flatten()}
		.join ( ch_peaks_bed_id )
		.set { ch_dt_peaks }
		//ch_dt_peaks \| view

		// ch_dt_peaks
		// .map { row -> row[1,2] }
		// .set { ch_ordered_bigwig }
		ch_dt_peaks
		.map { row -> row[1,2] }
		.set { ch_ordered_bigwig }
		//ch_ordered_bigwig \| view

		// ch_dt_peaks
		// .map { row -> row[-1] }
		// .set { ch_ordered_peaks_max }
		ch_dt_peaks
		.map { row -> row[-1] }
		.set { ch_ordered_peaks_max }
		//ch_ordered_peaks_max \| view

		/*
		* MODULE: Compute DeepTools matrix used in heatmap plotting for Genes
		*/
		// DEEPTOOLS_COMPUTEMATRIX_GENE (
		// ch_bigwig_no_igg,
		// PREPARE_GENOME.out.bed
		// )
		// ch_software_versions = ch_software_versions.mix(DEEPTOOLS_COMPUTEMATRIX_GENE.out.versions)
		DEEPTOOLS_COMPUTEMATRIX_GENE (
		ch_bigwig_no_igg,
		PREPARE_GENOME.out.bed
		)
		ch_software_versions = ch_software_versions.mix(DEEPTOOLS_COMPUTEMATRIX_GENE.out.versions)

		/*
		* MODULE: Calculate DeepTools heatmap
		*/
		// DEEPTOOLS_PLOTHEATMAP_GENE (
		// DEEPTOOLS_COMPUTEMATRIX_GENE.out.matrix
		// )
		// ch_software_versions = ch_software_versions.mix(DEEPTOOLS_PLOTHEATMAP_GENE.out.versions)
		DEEPTOOLS_PLOTHEATMAP_GENE (
		DEEPTOOLS_COMPUTEMATRIX_GENE.out.matrix
		)
		ch_software_versions = ch_software_versions.mix(DEEPTOOLS_PLOTHEATMAP_GENE.out.versions)

		// ch_ordered_peaks_max
		// .filter { it -> it.size() > 345}
		// .set { ch_ordered_peaks_max }
		// Run if not empty file size > 1 byte
		ch_ordered_peaks_max
		.filter { it -> it.size() > 1}
		.set { ch_ordered_peaks_max_notempty }
		//ch_ordered_peaks_max_notempty \| view

		/*
		* MODULE: Compute DeepTools matrix used in heatmap plotting for Peaks
		*/
		// DEEPTOOLS_COMPUTEMATRIX_PEAKS (
		// ch_ordered_bigwig,
		// ch_ordered_peaks_max
		// )
		DEEPTOOLS_COMPUTEMATRIX_PEAKS (
		ch_ordered_bigwig,
		ch_ordered_peaks_max_notempty
		)
		//EXAMPLE CHANNEL STRUCT: [[META], MATRIX]
		//DEEPTOOLS_COMPUTEMATRIX_PEAKS.out.matrix \| view

		/*
		* MODULE: Calculate DeepTools heatmap
		*/
		// DEEPTOOLS_PLOTHEATMAP_PEAKS (
		// DEEPTOOLS_COMPUTEMATRIX_PEAKS.out.matrix
		// )
		DEEPTOOLS_PLOTHEATMAP_PEAKS (
		DEEPTOOLS_COMPUTEMATRIX_PEAKS.out.matrix
		)
		}

		/*

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