Updates to get pipeline working after merge conflicts (d3420542) · Commits · Chaos / Cutandrun

workflows/cutandrun.nf

+17 −16

Original line number	Diff line number	Diff line
		@@ -303,7 +303,6 @@ include { CALCULATE_PEAK_REPROD } from "../modules/local/modules/calcu
		include { EXPORT_META } from "../modules/local/export_meta" addParams( options: modules["export_meta"] )
		include { EXPORT_META as EXPORT_META_CTRL } from "../modules/local/export_meta" addParams( options: modules["export_meta"] )
		include { GENERATE_REPORTS } from "../modules/local/python/generate_reports" addParams( options: modules["generate_reports"] )
		include { GET_SOFTWARE_VERSIONS } from "../modules/local/get_software_versions" addParams( options: [publish_files : ["csv":""]] )
		include { MULTIQC } from "../modules/local/multiqc" addParams( options: multiqc_options )

		/*
		@@ -342,6 +341,7 @@ include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_PEAKS } from "../mo
		include { DEEPTOOLS_PLOTHEATMAP as DEEPTOOLS_PLOTHEATMAP_GENE } from "../modules/nf-core/modules/deeptools/plotheatmap/main" addParams( options: modules["dt_plotheatmap_gene"] )
		include { DEEPTOOLS_PLOTHEATMAP as DEEPTOOLS_PLOTHEATMAP_PEAKS } from "../modules/nf-core/modules/deeptools/plotheatmap/main" addParams( options: modules["dt_plotheatmap_peaks"] )
		include { BEDTOOLS_INTERSECT } from "../modules/nf-core/modules/bedtools/intersect/main.nf" addParams( options: bedtools_intersect_options )
		include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/modules/custom/dumpsoftwareversions/main' addParams( options: [publish_files : ['_versions.yml':'']] )

		/*
		* SUBWORKFLOW: Consisting entirely of nf-core/modules
		@@ -627,7 +627,7 @@ workflow CUTANDRUN {
		ch_dummy_file,
		"bedGraph"
		)
		ch_software_versions = ch_software_versions.mix(BEDTOOLS_GENOMECOV_SCALE.out.versions)
		ch_software_versions = ch_software_versions.mix(BEDTOOLS_GENOMECOV.out.versions)
		//EXAMPLE CHANNEL STRUCT: [META], BEDGRAPH]
		//BEDTOOLS_GENOMECOV.out.genomecov \| view

		@@ -638,12 +638,13 @@ workflow CUTANDRUN {
		BEDTOOLS_GENOMECOV.out.genomecov,
		"bedGraph"
		)
		ch_software_versions = ch_software_versions.mix(BEDTOOLS_SORT.out.versions)

		/*
		* MODULE: Clip off bedgraphs so none overlap beyond chromosome edge
		*/
		UCSC_BEDCLIP (
		BEDTOOLS_SORT.out.sort,
		BEDTOOLS_SORT.out.sorted,
		PREPARE_GENOME.out.chrom_sizes
		)
		ch_software_versions = ch_software_versions.mix(UCSC_BEDCLIP.out.versions)
		@@ -664,7 +665,7 @@ workflow CUTANDRUN {
		/*
		* CHANNEL: Separate bedgraphs into target/control
		*/
		BEDTOOLS_SORT.out.sort.branch { it ->
		BEDTOOLS_SORT.out.sorted.branch { it ->
		target: it[0].group != "igg"
		control: it[0].group == "igg"
		}

Admin message