deduplication working (a9e12b17) · Commits · Chaos / Cutandrun

conf/modules.config

+34 −1

Original line number	Diff line number	Diff line
		@@ -333,7 +333,7 @@ if(params.run_mark_dups) {
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		pattern: "*.bam",
		enabled: ( params.save_align_intermed \|\| (!params.run_remove_dups) )
		enabled: ( params.save_align_intermed \|\| (!params.run_remove_dups) \|\| (!params.dedup_target_reads) )
		]
		}

		@@ -357,6 +357,39 @@ if(params.run_mark_dups) {
		}
		}

		if(params.run_remove_dups) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEDUPLICATE_PICARD:PICARD_MARKDUPLICATES' {
		ext.args = "--ASSUME_SORT_ORDER coordinate --REMOVE_DUPLICATES false --VALIDATION_STRINGENCY LENIENT --TMP_DIR tmp"
		ext.prefix = { "${meta.id}.target.dedup" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		pattern: "*.bam",
		enabled: true
		]
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEDUPLICATE_PICARD:SAMTOOLS_INDEX' {
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		pattern: "*.bai",
		enabled: true
		]
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEDUPLICATE_PICARD:BAM_STATS_SAMTOOLS:.*' {
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		pattern: "*.{stats,flagstat,idxstats}",
		enabled: true
		]
		}
		}
		}


		// "picard_dedup" {
		// args = "-ASSUME_SORT_ORDER coordinate -REMOVE_DUPLICATES true -VALIDATION_STRINGENCY LENIENT -TMP_DIR tmp"

workflows/cutandrun.nf

+18 −17

Original line number	Diff line number	Diff line
		@@ -167,7 +167,7 @@ include { CUSTOM_DUMPSOFTWAREVERSIONS } from "../mo
		* SUBWORKFLOW: Consisting entirely of nf-core/modules
		*/
		include { MARK_DUPLICATES_PICARD } from "../subworkflows/nf-core/mark_duplicates_picard"
		include { MARK_DUPLICATES_PICARD as DEDUP_PICARD } from "../subworkflows/nf-core/mark_duplicates_picard"
		include { MARK_DUPLICATES_PICARD as DEDUPLICATE_PICARD } from "../subworkflows/nf-core/mark_duplicates_picard"
		include { SAMTOOLS_VIEW_SORT_STATS } from "../subworkflows/nf-core/samtools_view_sort_stats"

		/*
		@@ -318,7 +318,7 @@ workflow CUTANDRUN {
		if (params.run_mark_dups) {
		MARK_DUPLICATES_PICARD (
		ch_samtools_bam,
		params.dedup_control_only
		false
		)
		ch_samtools_bam = MARK_DUPLICATES_PICARD.out.bam
		ch_samtools_bai = MARK_DUPLICATES_PICARD.out.bai
		@@ -334,19 +334,20 @@ workflow CUTANDRUN {
		/*
		* SUBWORKFLOW: Remove duplicates - default is on IgG controls only
		*/
		// ch_dedup_multiqc = Channel.empty()
		// if (run_remove_dups) {
		// DEDUP_PICARD (
		// ch_samtools_bam
		// )
		// ch_samtools_bam = DEDUP_PICARD.out.bam
		// ch_samtools_bai = DEDUP_PICARD.out.bai
		// ch_samtools_stats = DEDUP_PICARD.out.stats
		// ch_samtools_flagstat = DEDUP_PICARD.out.flagstat
		// ch_samtools_idxstats = DEDUP_PICARD.out.idxstats
		// ch_dedup_multiqc = DEDUP_PICARD.out.metrics
		// ch_software_versions = ch_software_versions.mix(DEDUP_PICARD.out.versions)
		// }
		ch_dedup_multiqc = Channel.empty()
		if (params.run_remove_dups) {
		DEDUPLICATE_PICARD (
		ch_samtools_bam,
		params.dedup_control_only
		)
		ch_samtools_bam = DEDUPLICATE_PICARD.out.bam
		ch_samtools_bai = DEDUPLICATE_PICARD.out.bai
		ch_samtools_stats = DEDUPLICATE_PICARD.out.stats
		ch_samtools_flagstat = DEDUPLICATE_PICARD.out.flagstat
		ch_samtools_idxstats = DEDUPLICATE_PICARD.out.idxstats
		ch_dedup_multiqc = DEDUPLICATE_PICARD.out.metrics
		ch_software_versions = ch_software_versions.mix(DEDUPLICATE_PICARD.out.versions)
		}
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false], [BAM]]
		//ch_samtools_bam \| view

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