corrected versioning CALCULATE_FRAGMENTS subworkflow (6a254f8d) · Commits · Chaos / Cutandrun

subworkflows/local/calculate_fragments.nf

+6 −3

Original line number	Diff line number	Diff line
		@@ -20,22 +20,27 @@ workflow CALCULATE_FRAGMENTS {
		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)

		// Convert to bed file
		BEDTOOLS_BAMTOBED ( SAMTOOLS_SORT.out.bam )
		ch_versions = ch_versions.mix(BEDTOOLS_BAMTOBED.out.versions)

		// Keep the read pairs that are on the same chromosome and fragment length less than 1000bp.
		AWK ( BEDTOOLS_BAMTOBED.out.bed )
		ch_versions = ch_versions.mix(AWK.out.versions)

		// Only extract the fragment related columns
		CUT ( AWK.out.file )
		@@ -44,7 +49,5 @@ workflow CALCULATE_FRAGMENTS {
		bed = CUT.out.file // channel: [ val(meta), [ bed ] ]
		bam = SAMTOOLS_SORT.out.bam // channel: [ val(meta), [ bam ] ]

		samtools_versions = SAMTOOLS_SORT.out.versions // path: *.version.txt
		bedtools_versions = BEDTOOLS_BAMTOBED.out.versions // path: *.version.txt
		awk_versions = AWK.out.versions // path: *.version.txt
		versions = ch_versions // channel: [ versions.yml ]
		}

+1 −1

Original line number	Diff line number	Diff line
		@@ -806,7 +806,7 @@ workflow CUTANDRUN {
		CALCULATE_FRAGMENTS (
		ch_samtools_bam
		)
		ch_software_versions = ch_software_versions.mix(CALCULATE_FRAGMENTS.out.bedtools_versions)
		ch_software_versions = ch_software_versions.mix(CALCULATE_FRAGMENTS.out.versions)
		//EXAMPLE CHANNEL STRUCT: NO CHANGE
		//CALCULATE_FRAGMENTS.out.bed \| view