corrected versioning ALIGN_BOWTIE2 subworkflow (d0909444) · Commits · Chaos / Cutandrun

subworkflows/local/align_bowtie2.nf

+8 −4

Original line number	Diff line number	Diff line
		@@ -19,10 +19,13 @@ workflow ALIGN_BOWTIE2 {
		spikein_index // channel: /path/to/bowtie2/spikein/index/

		main:
		ch_versions = Channel.empty()

		/*
		* Map reads with BOWTIE2 to target genome
		*/
		BOWTIE2_ALIGN ( reads, index )
		ch_versions = ch_versions.mix(BOWTIE2_ALIGN.out.versions)

		/*
		* Map reads with BOWTIE2 to spike-in genome
		@@ -33,11 +36,12 @@ workflow ALIGN_BOWTIE2 {
		* Sort, index BAM file and run samtools stats, flagstat and idxstats
		*/
		BAM_SORT_SAMTOOLS ( BOWTIE2_ALIGN.out.bam )
		ch_versions = ch_versions.mix(BAM_SORT_SAMTOOLS.out.versions)

		BAM_SORT_SAMTOOLS_SPIKEIN ( BOWTIE2_SPIKEIN_ALIGN.out.bam )

		emit:
		bowtie2_versions = BOWTIE2_ALIGN.out.versions // path: *.version.txt
		samtools_versions = BAM_SORT_SAMTOOLS.out.versions // path: *.version.txt
		versions = ch_versions // channel: [ versions.yml ]

		orig_bam = BOWTIE2_ALIGN.out.bam // channel: [ val(meta), bam ]
		orig_spikein_bam = BOWTIE2_SPIKEIN_ALIGN.out.bam // channel: [ val(meta), bam ]

+1 −1

Original line number	Diff line number	Diff line
		@@ -452,7 +452,7 @@ workflow CUTANDRUN {
		PREPARE_GENOME.out.bowtie2_index,
		PREPARE_GENOME.out.bowtie2_spikein_index
		)
		ch_software_versions = ch_software_versions.mix(ALIGN_BOWTIE2.out.bowtie2_versions)
		ch_software_versions = ch_software_versions.mix(ALIGN_BOWTIE2.out.versions)
		ch_orig_bam = ALIGN_BOWTIE2.out.orig_bam
		ch_orig_spikein_bam = ALIGN_BOWTIE2.out.orig_spikein_bam
		ch_bowtie2_log = ALIGN_BOWTIE2.out.bowtie2_log