Added ability to separately scale igg factor for deeptool normalisation (065dca4e) · Commits · Chaos / Cutandrun

modules.json

+0 −3

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

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

+2 −1

Original line number	Diff line number	Diff line
		@@ -8,7 +8,7 @@ process DEEPTOOLS_BAMCOVERAGE {
		'quay.io/biocontainers/deeptools:3.5.1--py_0' }"

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

		output:
		tuple val(meta), path("*.bigWig") , emit: bigwig, optional: true
		@@ -26,6 +26,7 @@ process DEEPTOOLS_BAMCOVERAGE {
		bamCoverage \
		--bam $input \
		$args \
		--scaleFactor ${scale} \
		--numberOfProcessors ${task.cpus} \
		--outFileName ${prefix}

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

+0 −0

File moved.

View file

nextflow.config

+1 −0

Original line number	Diff line number	Diff line
		@@ -60,6 +60,7 @@ params {
		normalisation_mode = "Spikein"
		normalisation_binsize = 1
		normalisation_c = 10000
		igg_scale_factor = 1

		// Peak Caller default param
		peakcaller = null

subworkflows/nf-core/prepare_peakcalling.nf

+42 −2

Original line number	Diff line number	Diff line
		@@ -3,7 +3,7 @@
		*/

		include { BEDTOOLS_GENOMECOV } from "../../modules/nf-core/modules/bedtools/genomecov/main"
		include { DEEPTOOLS_BAMCOVERAGE } from "../../modules/nf-core/modules/deeptools/bamcoverage/main"
		include { DEEPTOOLS_BAMCOVERAGE } from "../../modules/local/modules/deeptools/bamcoverage/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"
		@@ -94,11 +94,51 @@ workflow PREPARE_PEAKCALLING {
		// EXAMPLE CHANNEL STRUCT: [[META], BAM, BAI]
		//ch_bam_bai \| view

		/*
		* CHANNEL: Split files based on igg or not
		*/
		ch_bam_bai.branch { it ->
		target: it[0].group != "igg"
		control: it[0].group == "igg"
		}
		.set { ch_bam_bai_split }

		/*
		* CHANNEL: Assign scale factor of 1 to target files
		*/
		ch_bam_bai_split.target
		.map { row ->
		[ row[0], row[1], row[2], 1 ]
		}
		.set { ch_bam_bai_split_target }
		// EXAMPLE CHANNEL STRUCT: [[META], BAM, BAI, SCALE_FACTOR]
		//ch_bam_bai_split_target \| view

		/*
		* CHANNEL: Assign igg scale factor to target files
		*/
		ch_bam_bai_split.control
		.map { row ->
		[ row[0], row[1], row[2], params.igg_scale_factor ]
		}
		.set { ch_bam_bai_split_igg }
		// EXAMPLE CHANNEL STRUCT: [[META], BAM, BAI, SCALE_FACTOR]
		//ch_bam_bai_split_igg \| view

		/*
		* CHANNEL: Mix the split channels back up
		*/
		ch_bam_bai_split_target
		.mix(ch_bam_bai_split_igg)
		.set { ch_bam_bai_scale_factor }
		// EXAMPLE CHANNEL STRUCT: [[META], BAM, BAI, SCALE_FACTOR]
		//ch_bam_bai_scale_factor \| view

		/*
		* MODULE: Convert bam files to bedgraph and normalise
		*/
		DEEPTOOLS_BAMCOVERAGE (
		ch_bam_bai
		ch_bam_bai_scale_factor
		)
		ch_versions = ch_versions.mix(DEEPTOOLS_BAMCOVERAGE.out.versions)
		ch_bedgraph = DEEPTOOLS_BAMCOVERAGE.out.bedgraph

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