corrected versioning MARK_DUPLICATES_PICARD subworkflow (14518d54) · Commits · Chaos / Cutandrun

subworkflows/nf-core/mark_duplicates_picard.nf

+19 −17

Original line number	Diff line number	Diff line
		@@ -20,12 +20,12 @@ workflow MARK_DUPLICATES_PICARD {
		*/
		ch_bam = Channel.empty()
		metrics = Channel.empty()
		versions = Channel.empty()
		ch_versions = Channel.empty()
		if( !params.control_only ) {
		PICARD_MARKDUPLICATES ( bam )
		ch_bam = PICARD_MARKDUPLICATES.out.bam
		metrics = PICARD_MARKDUPLICATES.out.metrics
		versions = PICARD_MARKDUPLICATES.out.versions
		ch_versions = ch_versions.mix(PICARD_MARKDUPLICATES.out.versions)
		}
		else { // Split out non igg files and run only on these
		bam.branch { it ->
		@@ -35,9 +35,9 @@ workflow MARK_DUPLICATES_PICARD {
		.set { ch_split }

		PICARD_MARKDUPLICATES ( ch_split.control )
		metrics = PICARD_MARKDUPLICATES.out.metrics
		versions = PICARD_MARKDUPLICATES.out.versions
		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

		@@ -45,6 +45,7 @@ workflow MARK_DUPLICATES_PICARD {
		* Index BAM file
		*/
		SAMTOOLS_INDEX ( ch_bam )
		ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions)

		// Join bam/bai
		ch_bam
		@@ -58,15 +59,16 @@ workflow MARK_DUPLICATES_PICARD {
		* Run samtools stats, flagstat and idxstats
		*/
		BAM_STATS_SAMTOOLS ( ch_bam_bai )
		ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions)

		emit:
		bam = ch_bam // channel: [ val(meta), [ bam ] ]
		metrics // channel: [ val(meta), [ metrics ] ]
		picard_versions = versions // path: *.version.txt

		bai = SAMTOOLS_INDEX.out.bai // channel: [ val(meta), [ bai ] ]
		stats = BAM_STATS_SAMTOOLS.out.stats // channel: [ val(meta), [ stats ] ]
		flagstat = BAM_STATS_SAMTOOLS.out.flagstat // channel: [ val(meta), [ flagstat ] ]
		idxstats = BAM_STATS_SAMTOOLS.out.idxstats // channel: [ val(meta), [ idxstats ] ]
		samtools_versions = SAMTOOLS_INDEX.out.versions // path: *.version.txt

		versions = ch_versions // channel: [ versions.yml ]
		}

workflows/cutandrun.nf

+2 −1

Original line number	Diff line number	Diff line
		@@ -503,7 +503,7 @@ workflow CUTANDRUN {
		ch_samtools_flagstat = MARK_DUPLICATES_PICARD.out.flagstat
		ch_samtools_idxstats = MARK_DUPLICATES_PICARD.out.idxstats
		ch_markduplicates_metrics = MARK_DUPLICATES_PICARD.out.metrics
		ch_software_versions = ch_software_versions.mix(MARK_DUPLICATES_PICARD.out.picard_versions)
		ch_software_versions = ch_software_versions.mix(MARK_DUPLICATES_PICARD.out.versions)
		}
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false], [BAM]]
		//ch_samtools_bam \| view
		@@ -522,6 +522,7 @@ workflow CUTANDRUN {
		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)
		}
		//EXAMPLE CHANNEL STRUCT: [[id:h3k27me3_R1, group:h3k27me3, replicate:1, single_end:false], [BAM]]
		//ch_samtools_bam \| view

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