corrected versioning bam_sort_samtools subworkflow (d7fb0ffe) · Commits · Chaos / Cutandrun

subworkflows/nf-core/bam_sort_samtools.nf

+5 −1

Original line number	Diff line number	Diff line
		@@ -14,15 +14,18 @@ workflow BAM_SORT_SAMTOOLS {
		ch_bam // channel: [ val(meta), [ bam ] ]

		main:
		ch_versions = Channel.empty()
		/*
		* SORT BAM file
		*/
		SAMTOOLS_SORT ( ch_bam )
		ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions)

		/*
		* Index BAM file
		*/
		SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam )
		ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions)

		// Join bam/bai
		ch_bam_sample_id = SAMTOOLS_SORT.out.bam.map { row -> [row[0].id, row] }
		@@ -33,6 +36,7 @@ workflow BAM_SORT_SAMTOOLS {
		* Run samtools stats, flagstat and idxstats
		*/
		BAM_STATS_SAMTOOLS ( ch_bam_bai )
		ch_versions = ch_versions.mix(BAM_STATS_SAMTOOLS.out.versions)

		emit:
		bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ]
		@@ -40,5 +44,5 @@ workflow BAM_SORT_SAMTOOLS {
		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 ] ]
		versions = SAMTOOLS_SORT.out.versions // path: *.version.txt
		versions = ch_versions // channel: [ versions.yml ]
		}