corrected versioning SAMTOOLS_VIEW_SORT_STATS subworkflow (8fcd57fd) · Commits · Chaos / Cutandrun

subworkflows/nf-core/samtools_view_sort_stats.nf

+11 −6

Original line number	Diff line number	Diff line
		@@ -16,20 +16,24 @@ workflow SAMTOOLS_VIEW_SORT_STATS {
		bam // channel: [ val(meta), [ bam ] ]

		main:
		ch_versions = Channel.empty()
		/*
		* Filter BAM file
		*/
		SAMTOOLS_VIEW ( bam )
		ch_versions = ch_versions.mix(SAMTOOLS_VIEW.out.versions)

		/*
		* Sort BAM file
		*/
		SAMTOOLS_SORT ( SAMTOOLS_VIEW.out.bam )
		ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions)

		/*
		* Index BAM file and run samtools stats, flagstat and idxstats
		*/
		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] }
		@@ -37,6 +41,7 @@ workflow SAMTOOLS_VIEW_SORT_STATS {
		ch_bam_bai = ch_bam_sample_id.join(ch_bai_sample_id, by: [0]).map {row -> [row[1][0], row[1][1], row[2][1]]}

		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 ] ]
		@@ -44,5 +49,5 @@ workflow SAMTOOLS_VIEW_SORT_STATS {
		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 ]
		}