Included software versioning for all modules and subworkflows run (edb78acb) · Commits · Chaos / Cutandrun

workflows/cutandrun.nf

+13 −3

Original line number	Diff line number	Diff line
		@@ -722,6 +722,7 @@ workflow CUTANDRUN {
		params.peak_threshold
		)
		ch_seacr_bed = SEACR_CALLPEAK_NOIGG.out.bed
		ch_software_versions = ch_software_versions.mix(SEACR_CALLPEAK_NOIGG.out.versions)
		//ch_software_versions = ch_software_versions.mix(SEACR_NO_IGG.out.versions)
		// EXAMPLE CHANNEL STRUCT: [[META], BED]
		//SEACR_NO_IGG.out.bed \| view
		@@ -733,6 +734,7 @@ workflow CUTANDRUN {
		AWK_NAME_PEAK_BED (
		ch_seacr_bed
		)
		ch_software_versions = ch_software_versions.mix(AWK_NAME_PEAK_BED.out.versions)
		// EXAMPLE CHANNEL STRUCT: [[META], BED]
		//AWK_NAME_PEAK_BED.out.file \| view

		@@ -843,6 +845,7 @@ workflow CUTANDRUN {
		SAMTOOLS_CUSTOMVIEW (
		ch_bam_bai
		)
		ch_software_versions = ch_software_versions.mix(SAMTOOLS_CUSTOMVIEW.out.versions)
		//SAMTOOLS_CUSTOMVIEW.out.tsv \| view
		}

		@@ -865,6 +868,7 @@ workflow CUTANDRUN {
		ch_seacr_bed.collect{it[1]}.ifEmpty([]),
		UCSC_BEDGRAPHTOBIGWIG.out.bigwig.collect{it[1]}.ifEmpty([])
		)
		ch_software_versions = ch_software_versions.mix(IGV_SESSION.out.versions)
		}

		if (run_deep_tools){
		@@ -874,6 +878,7 @@ workflow CUTANDRUN {
		AWK_EDIT_PEAK_BED (
		ch_seacr_bed
		)
		ch_software_versions = ch_software_versions.mix(AWK_EDIT_PEAK_BED.out.versions)
		//AWK_EDIT_PEAK_BED.out.file \| view

		/*
		@@ -918,7 +923,7 @@ workflow CUTANDRUN {
		DEEPTOOLS_PLOTHEATMAP_GENE (
		DEEPTOOLS_COMPUTEMATRIX_GENE.out.matrix
		)

		ch_software_versions = ch_software_versions.mix(DEEPTOOLS_PLOTHEATMAP_GENE.out.versions)
		/*
		* MODULE: Compute DeepTools matrix used in heatmap plotting for Peaks
		*/
		@@ -955,6 +960,7 @@ workflow CUTANDRUN {
		CALCULATE_FRIP (
		ch_bam_bai_bed
		)
		ch_software_versions = ch_software_versions.mix(CALCULATE_FRIP.out.versions)

		/*
		* SUBWORKFLOW: Annotate meta-data with frip stats
		@@ -965,6 +971,7 @@ workflow CUTANDRUN {
		)
		ch_samtools_bam_ctrl = ch_samtools_bam
		ch_samtools_bam = ANNOTATE_FRIP_META.out.output
		ch_software_versions = ch_software_versions.mix(ANNOTATE_FRIP_META.out.versions)
		//ch_samtools_bam \| view

		/*
		@@ -992,6 +999,7 @@ workflow CUTANDRUN {
		ch_beds_intersect,
		"bed"
		)
		ch_software_versions = ch_software_versions.mix(BEDTOOLS_INTERSECT.out.versions)
		//EXAMPLE CHANNEL STRUCT: [[META], BED]
		//BEDTOOLS_INTERSECT.out.intersect \| view

		@@ -1001,6 +1009,7 @@ workflow CUTANDRUN {
		CALCULATE_PEAK_REPROD (
		BEDTOOLS_INTERSECT.out.intersect
		)
		ch_software_versions = ch_software_versions.mix(CALCULATE_PEAK_REPROD.out.versions)
		//EXAMPLE CHANNEL STRUCT: [[META], CSV]
		//CALCULATE_PEAK_REPROD.out.csv

		@@ -1012,6 +1021,7 @@ workflow CUTANDRUN {
		CALCULATE_PEAK_REPROD.out.csv
		)
		ch_samtools_bam = ANNOTATE_PEAK_REPRO_META.out.output
		ch_software_versions = ch_software_versions.mix(ANNOTATE_PEAK_REPRO_META.out.versions)
		//ch_samtools_bam \| view

		/*

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