Fix for bt2 update (1795392b) · Commits · Chaos / Cutandrun

subworkflows/local/align_bowtie2.nf

+2 −2

Original line number	Diff line number	Diff line
		@@ -19,13 +19,13 @@ workflow ALIGN_BOWTIE2 {
		/*
		* Map reads with BOWTIE2 to target genome
		*/
		BOWTIE2_ALIGN ( reads, index, params.save_unaligned )
		BOWTIE2_ALIGN ( reads, index, params.save_unaligned, false )
		ch_versions = ch_versions.mix(BOWTIE2_ALIGN.out.versions)

		/*
		* Map reads with BOWTIE2 to spike-in genome
		*/
		BOWTIE2_SPIKEIN_ALIGN ( reads, spikein_index, params.save_unaligned )
		BOWTIE2_SPIKEIN_ALIGN ( reads, spikein_index, params.save_unaligned, false )

		/*
		* Sort, index BAM file and run samtools stats, flagstat and idxstats