corrected versioning CONSENSUS_PEAKS workflow (d26a5586) · Commits · Chaos / Cutandrun

subworkflows/local/consensus_peaks.nf

+8 −1

Original line number	Diff line number	Diff line
		@@ -19,23 +19,30 @@ workflow CONSENSUS_PEAKS {
		bed // channel: [ val(meta), [ bed ], count]

		main:
		ch_versions = Channel.empty()

		// Sort bed files
		SORT ( bed )
		ch_versions = ch_versions.mix(SORT.out.versions)


		// Merge peaks
		BEDTOOLS_MERGE ( SORT.out.file )
		ch_versions = ch_versions.mix(BEDTOOLS_MERGE.out.versions)

		// Filter peaks on minimum replicate consensus
		AWK ( BEDTOOLS_MERGE.out.bed )
		ch_versions = ch_versions.mix(AWK.out.versions)

		// Plot consensus peak sets
		if(params.run_peak_plotting) {
		PLOT_CONSENSUS_PEAKS ( BEDTOOLS_MERGE.out.bed.collect{it[1]}.ifEmpty([]) )
		ch_versions = ch_versions.mix(PLOT_CONSENSUS_PEAKS.out.versions)

		}

		emit:
		bed = BEDTOOLS_MERGE.out.bed // channel: [ val(meta), [ bed ] ]
		filtered_bed = AWK.out.file // channel: [ val(meta), [ bed ] ]
		bedtools_versions = BEDTOOLS_MERGE.out.versions // path: *.version.txt
		versions = ch_versions // channel: [ versions.yml ]
		}

+4 −0

Original line number	Diff line number	Diff line
		@@ -761,6 +761,8 @@ workflow CUTANDRUN {
		CONSENSUS_PEAKS_ALL (
		ch_seacr_bed_all
		)
		ch_software_versions = ch_software_versions.mix(CONSENSUS_PEAKS_ALL.out.versions)

		// EXAMPLE CHANNEL STRUCT: [[META], BED]
		//CONSENSUS_PEAKS_ALL.out.bed \| view

		@@ -793,6 +795,8 @@ workflow CUTANDRUN {
		CONSENSUS_PEAKS (
		ch_seacr_bed_group
		)
		ch_software_versions = ch_software_versions.mix(CONSENSUS_PEAKS.out.versions)

		// EXAMPLE CHANNEL STRUCT: [[META], BED]
		//CONSENSUS_PEAKS.out.bed \| view