pre-peak processing (516298ce) · Commits · Chaos / Cutandrun

conf/modules.config

+58 −31

Original line number	Diff line number	Diff line
		@@ -421,17 +421,66 @@ process {
		}
		}

		/*
		========================================================================================
		SCALING/CONVERSION AND PEAK CALLING
		========================================================================================
		*/

		if(params.run_peak_calling) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:BEDTOOLS_GENOMECOV' {
		publishDir = [
		enabled: false
		]
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:BEDTOOLS_SORT' {
		ext.prefix = { "${meta.id}.sorted" }
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/01_bam_to_bedgraph" },
		mode: 'copy',
		pattern: "*.bedGraph",
		enabled: true
		]
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:UCSC_BEDCLIP' {
		ext.prefix = { "${meta.id}.clipped" }
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/02_clip_bed" },
		mode: 'copy',
		pattern: "*.bedGraph",
		enabled: true
		]
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:UCSC_BEDGRAPHTOBIGWIG' {
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/03_bed_to_bigwig" },
		mode: 'copy',
		pattern: "*.bigwig",
		enabled: true
		]
		}
		}
		}

		// "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"
		// }




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



		@@ -442,45 +491,23 @@ process {



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










		// /*
		// ========================================================================================
		// SCALING/CONVERSION AND PEAK CALLING
		// ========================================================================================
		// */

		// "bedtools_genomecov_bedgraph" {
		// //publish_dir = "03_peak_calling/01_bam_to_bedgraph"
		// publish_files = false
		// }

		// "sort_bedgraph" {
		// publish_dir = "03_peak_calling/01_bam_to_bedgraph"
		// suffix = ".sorted"
		// }

		// "ucsc_bedclip" {
		// suffix = ".clipped"
		// publish_dir = "03_peak_calling/02_clip_bed"
		// }

		// "ucsc_bedgraphtobigwig" {
		// publish_dir = "03_peak_calling/03_bed_to_bigwig"
		// }

		// "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"
		// }

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

workflows/cutandrun.nf

+55 −55

Original line number	Diff line number	Diff line
		@@ -148,10 +148,10 @@ include { ANNOTATE_META_AWK as ANNOTATE_DEDUP_META } from "../subworkflows
		* MODULES
		*/
		include { CAT_FASTQ } from "../modules/nf-core/modules/cat/fastq/main"
		// include { BEDTOOLS_GENOMECOV } from "../modules/nf-core/modules/bedtools/genomecov/main" addParams( options: modules["bedtools_genomecov_bedgraph"] )
		// include { BEDTOOLS_SORT } from "../modules/nf-core/modules/bedtools/sort/main" addParams( options: modules["sort_bedgraph"] )
		// include { UCSC_BEDCLIP } from "../modules/nf-core/modules/ucsc/bedclip/main" addParams( options: modules["ucsc_bedclip"] )
		// include { UCSC_BEDGRAPHTOBIGWIG } from "../modules/nf-core/modules/ucsc/bedgraphtobigwig/main" addParams( options: modules["ucsc_bedgraphtobigwig"] )
		include { BEDTOOLS_GENOMECOV } from "../modules/nf-core/modules/bedtools/genomecov/main"
		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 )
		@@ -407,43 +407,43 @@ workflow CUTANDRUN {
		* CHANNEL: Calculate scale factor for each sample based on a constant devided by the number
		* of reads aligned to the spike-in genome.
		*/
		// if (!params.skip_scale) {
		// ch_samtools_bam
		// .map { row ->
		// def denominator = row[0].find{ it.key == "bt2_total_aligned_spikein" }?.value.toInteger()
		// [ row[0].id, params.normalisation_c / (denominator != 0 ? denominator : 1) ]
		// }
		// .set { ch_scale_factor }
		// } else {
		// ch_samtools_bam
		// .map { row ->
		// [ row[0].id, 1 ]
		// }
		// .set { ch_scale_factor }
		// }
		if (!params.skip_scale) {
		ch_samtools_bam
		.map { row ->
		def denominator = row[0].find{ it.key == "bt2_total_aligned_spikein" }?.value.toInteger()
		[ row[0].id, params.normalisation_c / (denominator != 0 ? denominator : 1) ]
		}
		.set { ch_scale_factor }
		} else {
		ch_samtools_bam
		.map { row ->
		[ row[0].id, 1 ]
		}
		.set { ch_scale_factor }
		}
		// EXAMPLE CHANNEL STRUCT: [id, scale_factor]
		//ch_scale_factor \| view

		/*
		* CHANNEL: Create a channel with the scale factor as a seperate value
		*/
		// ch_samtools_bam
		// .map { row -> [row[0].id, row ].flatten()}
		// .join ( ch_scale_factor )
		// .map { row -> row[1..(row.size() - 1)] }
		// .map { row ->
		// row[0].put("scale_factor", row[2])
		// [ row[0], row[1], row[2] ] }
		// .set { ch_samtools_bam_scale }
		ch_samtools_bam
		.map { row -> [row[0].id, row ].flatten()}
		.join ( ch_scale_factor )
		.map { row -> row[1..(row.size() - 1)] }
		.map { row ->
		row[0].put("scale_factor", row[2])
		[ row[0], row[1], row[2] ] }
		.set { ch_samtools_bam_scale }
		//EXAMPLE CHANNEL STRUCT: [[META + scale_factor:10000], BAM, SCALE_FACTOR]
		//ch_samtools_bam_scale \| view

		/*
		* CHANNEL: Add the scale factor values to the main meta-data stream
		*/
		// ch_samtools_bam_scale
		// .map { row -> [ row[0], row[1] ] }
		// .set { ch_samtools_bam }
		ch_samtools_bam_scale
		.map { row -> [ row[0], row[1] ] }
		.set { ch_samtools_bam }
		//EXAMPLE CHANNEL STRUCT: [[META], BAM]
		//ch_samtools_bam \| view

		@@ -451,54 +451,54 @@ workflow CUTANDRUN {
		/*
		* MODULE: Convert bam files to bedgraph
		*/
		// BEDTOOLS_GENOMECOV (
		// ch_samtools_bam_scale,
		// ch_dummy_file,
		// "bedGraph"
		// )
		// ch_software_versions = ch_software_versions.mix(BEDTOOLS_GENOMECOV.out.versions)
		BEDTOOLS_GENOMECOV (
		ch_samtools_bam_scale,
		ch_dummy_file,
		"bedGraph"
		)
		ch_software_versions = ch_software_versions.mix(BEDTOOLS_GENOMECOV.out.versions)
		//EXAMPLE CHANNEL STRUCT: [META], BEDGRAPH]
		//BEDTOOLS_GENOMECOV.out.genomecov \| view

		/*
		* MODULE: Sort bedgraph
		*/
		// BEDTOOLS_SORT (
		// BEDTOOLS_GENOMECOV.out.genomecov,
		// "bedGraph"
		// )
		// ch_software_versions = ch_software_versions.mix(BEDTOOLS_SORT.out.versions)
		BEDTOOLS_SORT (
		BEDTOOLS_GENOMECOV.out.genomecov,
		"bedGraph"
		)
		ch_software_versions = ch_software_versions.mix(BEDTOOLS_SORT.out.versions)

		/*
		* MODULE: Clip off bedgraphs so none overlap beyond chromosome edge
		*/
		// UCSC_BEDCLIP (
		// BEDTOOLS_SORT.out.sorted,
		// PREPARE_GENOME.out.chrom_sizes
		// )
		// ch_software_versions = ch_software_versions.mix(UCSC_BEDCLIP.out.versions)
		UCSC_BEDCLIP (
		BEDTOOLS_SORT.out.sorted,
		PREPARE_GENOME.out.chrom_sizes
		)
		ch_software_versions = ch_software_versions.mix(UCSC_BEDCLIP.out.versions)
		//EXAMPLE CHANNEL STRUCT: [META], BEDGRAPH]
		//UCSC_BEDCLIP.out.bedgraph \| view

		/*
		* MODULE: Convert bedgraph to bigwig
		*/
		// UCSC_BEDGRAPHTOBIGWIG (
		// UCSC_BEDCLIP.out.bedgraph,
		// PREPARE_GENOME.out.chrom_sizes
		// )
		// ch_software_versions = ch_software_versions.mix(UCSC_BEDGRAPHTOBIGWIG.out.versions)
		UCSC_BEDGRAPHTOBIGWIG (
		UCSC_BEDCLIP.out.bedgraph,
		PREPARE_GENOME.out.chrom_sizes
		)
		ch_software_versions = ch_software_versions.mix(UCSC_BEDGRAPHTOBIGWIG.out.versions)
		//EXAMPLE CHANNEL STRUCT: [[META], BIGWIG]
		//UCSC_BEDGRAPHTOBIGWIG.out.bigwig \| view

		/*
		* CHANNEL: Separate bedgraphs into target/control
		*/
		// BEDTOOLS_SORT.out.sorted.branch { it ->
		// target: it[0].group != "igg"
		// control: it[0].group == "igg"
		// }
		// .set { ch_bedgraph_split }
		BEDTOOLS_SORT.out.sorted.branch { it ->
		target: it[0].group != "igg"
		control: it[0].group == "igg"
		}
		.set { ch_bedgraph_split }
		//ch_bedgraph_split.target \| view
		//ch_bedgraph_split.control \| view

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