Fixed igg control splitting (812fe226) · Commits · Chaos / Cutandrun

conf/flowswitch.config

+0 −3

Original line number	Diff line number	Diff line
		@@ -25,13 +25,10 @@ params {
		run_multiqc = true
		run_peak_plotting = true
		run_igv = true

		dedup_control_only = true
		}

		params.callers = params.peakcaller ? params.peakcaller.split(',').collect{ it.trim().toLowerCase() } : ['seacr']

		if(params.dedup_target_reads) { params.dedup_control_only = false }
		if(params.consensus_peak_mode == 'all') { params.run_consensus_all = true }

		if(params.minimum_alignment_q_score > 0) { params.run_q_filter = true }

subworkflows/local/input_check.nf

+1 −1

Original line number	Diff line number	Diff line
		@@ -27,7 +27,7 @@ def get_samplesheet_paths(LinkedHashMap row) {
		meta.id = row.id
		meta.group = row.group
		meta.replicate = row.replicate.toInteger()
		meta.control_group = row.control_group
		meta.control_group = row.control
		meta.single_end = row.single_end.toBoolean()
		meta.is_control = row.is_control.toBoolean()

subworkflows/nf-core/mark_duplicates_picard.nf

+9 −7

Original line number	Diff line number	Diff line
		@@ -9,7 +9,7 @@ include { BAM_STATS_SAMTOOLS } from './bam_stats_samtools'
		workflow MARK_DUPLICATES_PICARD {
		take:
		bam // channel: [ val(meta), [ bam ] ]
		control_only //boolean
		process_target //boolean

		main:
		/*
		@@ -18,25 +18,27 @@ workflow MARK_DUPLICATES_PICARD {
		ch_bam = Channel.empty()
		metrics = Channel.empty()
		ch_versions = Channel.empty()
		if( !control_only ) {
		if( process_target ) {
		PICARD_MARKDUPLICATES ( bam )
		ch_bam = PICARD_MARKDUPLICATES.out.bam
		metrics = PICARD_MARKDUPLICATES.out.metrics
		ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions)
		}
		else { // Split out non igg files and run only on these
		else { // Split out control files and run only on these
		bam.branch { it ->
		target: it[0].is_control == 0
		control: it[0].is_control == 1
		target: it[0].is_control == false
		control: it[0].is_control == true
		}
		.set { ch_split }
		//ch_split.target \| view
		//ch_split.control \| view

		PICARD_MARKDUPLICATES ( ch_split.control )
		ch_bam = PICARD_MARKDUPLICATES.out.bam.mix ( ch_split.target )
		metrics = PICARD_MARKDUPLICATES.out.metrics
		ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions)
		}
		//out_bam \| view
		//ch_bam \| view

		/*
		* Index BAM file

subworkflows/nf-core/prepare_peakcalling.nf

+2 −2

Original line number	Diff line number	Diff line
		@@ -98,8 +98,8 @@ workflow PREPARE_PEAKCALLING {
		* CHANNEL: Split files based on igg or not
		*/
		ch_bam_bai.branch { it ->
		target: it[0].is_control == 0
		control: it[0].is_control == 1
		target: it[0].is_control == false
		control: it[0].is_control == true
		}
		.set { ch_bam_bai_split }

workflows/cutandrun.nf

+9 −9

Original line number	Diff line number	Diff line
		@@ -304,7 +304,7 @@ workflow CUTANDRUN {
		if (params.run_mark_dups) {
		MARK_DUPLICATES_PICARD (
		ch_samtools_bam,
		false
		true
		)
		ch_samtools_bam = MARK_DUPLICATES_PICARD.out.bam
		ch_samtools_bai = MARK_DUPLICATES_PICARD.out.bai
		@@ -324,7 +324,7 @@ workflow CUTANDRUN {
		if (params.run_remove_dups) {
		DEDUPLICATE_PICARD (
		ch_samtools_bam,
		params.dedup_control_only
		params.dedup_target_reads
		)
		ch_samtools_bam = DEDUPLICATE_PICARD.out.bam
		ch_samtools_bai = DEDUPLICATE_PICARD.out.bai
		@@ -411,8 +411,8 @@ workflow CUTANDRUN {
		* CHANNEL: Separate bedgraphs into target/control
		*/
		ch_bedgraph.branch { it ->
		target: it[0].is_control == 0
		control: it[0].is_control == 1
		target: it[0].is_control == false
		control: it[0].is_control == true
		}
		.set { ch_bedgraph_split }
		//ch_bedgraph_split.target \| view
		@@ -465,8 +465,8 @@ workflow CUTANDRUN {

		if('macs2' in callers) {
		ch_samtools_bam.branch{ it ->
		target: it[0].is_control == 0
		control: it[0].is_control == 1
		target: it[0].is_control == false
		control: it[0].is_control == true
		}
		.set { ch_samtools_bam_split }
		// ch_samtools_bam_split.target \| view
		@@ -532,8 +532,8 @@ workflow CUTANDRUN {

		if('macs2' in callers) {
		ch_samtools_bam.branch{ it ->
		target: it[0].is_control == 0
		control: it[0].is_control == 1
		target: it[0].is_control == false
		control: it[0].is_control == true
		}
		.set { ch_samtools_bam_split }
		// ch_samtools_bam_split.target \| view
		@@ -724,7 +724,7 @@ workflow CUTANDRUN {
		* CHANNEL: Remove IgG from bigwig channel
		*/
		ch_bigwig
		.filter { it[0].is_control == 0 }
		.filter { it[0].is_control == false }
		.set { ch_bigwig_no_igg }
		//ch_bigwig_no_igg \| view

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