Fixed another context issue (140db94a) · Commits · Chaos / Cutandrun

subworkflows/nf-core/mark_duplicates_picard.nf

+6 −8

Original line number	Diff line number	Diff line
		@@ -18,12 +18,12 @@ workflow MARK_DUPLICATES_PICARD {
		/*
		* Picard MarkDuplicates
		*/
		out_bam = Channel.empty()
		ch_bam = Channel.empty()
		metrics = Channel.empty()
		version = Channel.empty()
		if( !params.control_only ) {
		PICARD_MARKDUPLICATES ( bam )
		out_bam = PICARD_MARKDUPLICATES.out.bam
		ch_bam = PICARD_MARKDUPLICATES.out.bam
		metrics = PICARD_MARKDUPLICATES.out.metrics
		version = PICARD_MARKDUPLICATES.out.version
		}
		@@ -35,21 +35,19 @@ workflow MARK_DUPLICATES_PICARD {
		.set { ch_split }

		PICARD_MARKDUPLICATES ( ch_split.control )
		out_bam = PICARD_MARKDUPLICATES.out.bam
		metrics = PICARD_MARKDUPLICATES.out.metrics
		version = PICARD_MARKDUPLICATES.out.version

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

		/*
		* Index BAM file
		*/
		SAMTOOLS_INDEX ( out_bam )
		SAMTOOLS_INDEX ( ch_bam )

		// Join bam/bai
		out_bam
		ch_bam
		.map { row -> [row[0].id, row ].flatten()}
		.join ( SAMTOOLS_INDEX.out.bai.map { row -> [row[0].id, row ].flatten()} )
		.map { row -> [row[1], row[2], row[4]] }
		@@ -62,7 +60,7 @@ workflow MARK_DUPLICATES_PICARD {
		BAM_STATS_SAMTOOLS ( ch_bam_bai )

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