Switching to nf-core bedtools genomecov (30d47964) · Commits · Chaos / Cutandrun

conf/modules.config

+6 −0

Original line number	Diff line number	Diff line
		@@ -141,7 +141,13 @@ params {
		*/

		"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" {

modules.json

+3 −0

Original line number	Diff line number	Diff line
		@@ -15,6 +15,9 @@
		"bedtools/merge": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		},
		"bedtools/sort": {
		"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
		},
		"bowtie2/align": {
		"git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
		},

workflows/cutandrun.nf

+40 −29

Original line number	Diff line number	Diff line
		@@ -293,8 +293,6 @@ multiqc_options.args += params.multiqc_title ? " --title \"$params.multiqc_title
		* MODULES
		*/
		include { INPUT_CHECK } from "../subworkflows/local/input_check" addParams( options: [:] )
		include { CAT_FASTQ } from "../modules/nf-core/modules/cat/fastq/main" addParams( options: cat_fastq_options )
		include { BEDTOOLS_GENOMECOV_SCALE } from "../modules/local/bedtools_genomecov_scale" addParams( options: modules["bedtools_genomecov_bedgraph"] )
		include { AWK as AWK_NAME_PEAK_BED } from "../modules/local/linux/awk" addParams( options: modules["awk_name_peak_bed"] )
		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"] )
		@@ -332,6 +330,9 @@ include { ANNOTATE_META_CSV as ANNOTATE_PEAK_REPRO_META } from "../subworkflows
		/*
		* MODULES
		*/
		include { CAT_FASTQ } from "../modules/nf-core/modules/cat/fastq/main" addParams( options: cat_fastq_options )
		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 { SEACR_CALLPEAK } from "../modules/nf-core/modules/seacr/callpeak/main" addParams( options: modules["seacr"] )
		@@ -613,17 +614,27 @@ workflow CUTANDRUN {
		/*
		* MODULE: Convert bam files to bedgraph
		*/
		BEDTOOLS_GENOMECOV_SCALE (
		ch_samtools_bam_scale
		BEDTOOLS_GENOMECOV (
		ch_samtools_bam_scale,
		ch_dummy_file,
		"bedgraph"
		)
		//EXAMPLE CHANNEL STRUCT: [META], BEDGRAPH]
		//BEDTOOLS_GENOMECOV_SCALE.out.bedgraph \| view
		//BEDTOOLS_GENOMECOV.out.genomecov \| view

		/*
		* MODULE: Sort bedgraph
		*/
		BEDTOOLS_SORT (
		BEDTOOLS_GENOMECOV.out.genomecov,
		"bedgraph"
		)

		/*
		* MODULE: Clip off bedgraphs so none overlap beyond chromosome edge
		*/
		UCSC_BEDCLIP (
		BEDTOOLS_GENOMECOV_SCALE.out.bedgraph,
		BEDTOOLS_SORT.out.sort,
		PREPARE_GENOME.out.chrom_sizes
		)
		//EXAMPLE CHANNEL STRUCT: [META], BEDGRAPH]
		@@ -643,7 +654,7 @@ workflow CUTANDRUN {
		/*
		* CHANNEL: Separate bedgraphs into target/control
		*/
		BEDTOOLS_GENOMECOV_SCALE.out.bedgraph.branch { it ->
		BEDTOOLS_SORT.out.sort.branch { it ->
		target: it[0].group != "igg"
		control: it[0].group == "igg"
		}

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