Reporting activated but not working (c4d79e7a) · Commits · Chaos / Cutandrun

conf/modules.config

+74 −26

Original line number	Diff line number	Diff line
		@@ -723,42 +723,90 @@ if(params.run_reporting && params.run_deep_tools) {
		}
		}

		if(params.run_reporting) {
		process {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:CALCULATE_FRIP' {
		publishDir = [
		enabled: false
		]
		}

		// "export_meta" {
		// publish_dir = "04_reporting"
		// }
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:CUT_CALC_REPROD' {
		ext.args = "-f 1,2,3,6"
		ext.suffix = ".repro"
		ext.ext = "bed"
		publishDir = [
		enabled: false
		]
		}

		// "calc_frip" {
		// publish_files = false
		// }
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:BEDTOOLS_INTERSECT' {
		ext.args = "-C -sorted"
		publishDir = [
		enabled: false
		]
		}

		// "meta_csv_frip_options" {
		// publish_files = false
		// }
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:CALCULATE_PEAK_REPROD' {
		publishDir = [
		enabled: false
		]
		}

		// "bedtools_intersect" {
		// publish_files = false
		// }
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:EXPORT_META' {
		publishDir = [
		path: { "${params.outdir}/04_reporting" },
		mode: 'copy',
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		}

		// "calc_peak_repro_cut" {
		// args = "-f 1,2,3,6"
		// suffix = ".repro"
		// ext = "bed"
		// }
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:EXPORT_META_CTRL' {
		publishDir = [
		path: { "${params.outdir}/04_reporting" },
		mode: 'copy',
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:GENERATE_REPORTS' {
		publishDir = [
		path: { "${params.outdir}/04_reporting/qc" },
		mode: 'copy',
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		}

		// "calc_peak_repro" {
		// publish_files = false
		// }

		// "meta_csv_peak_repro_options" {
		// publish_files = false
		// }

		// "generate_reports" {
		// publish_dir = "04_reporting/qc"
		}
		}


		// if (!params.run_multiqc) {
		// process {
		// withName: MULTIQC {
		// ext.args = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
		// publishDir = [
		// path: { [
		// "${params.outdir}/multiqc",
		// params.skip_alignment? '' : "/${params.aligner}"
		// ].join('') },
		// mode: 'copy',
		// saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
		// ]
		// }
		// }
		// }

		// "multiqc" {
		// args = "-v"
		// publish_dir = "04_reporting/multiqc"
		// }

		// // Multi QC
		// def multiqc_options = modules["multiqc"]
		// multiqc_options.args += params.multiqc_title ? " --title \"$params.multiqc_title\"" : ""
		No newline at end of file

modules/local/export_meta.nf

+3 −3

Original line number	Diff line number	Diff line
		process EXPORT_META {
		label 'process_low'

		conda (params.enable_conda ? null : null)
		conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)
		container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
		'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
		'quay.io/biocontainers/biocontainers:v1.2.0_cv1' }"
		'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
		'quay.io/biocontainers/gawk:5.1.0' }"

		input:
		val meta

workflows/cutandrun.nf

+94 −103

Original line number	Diff line number	Diff line
		@@ -76,19 +76,6 @@ if ((caller_list + callers).unique().size() != caller_list.size()) {
		exit 1, "Invalid variant calller option: ${params.peakcaller}. Valid options: ${caller_list.join(', ')}"
		}

		// // Meta annotation options
		// def awk_bt2_options = modules["awk_bt2"]
		// def awk_bt2_spikein_options = modules["awk_bt2_spikein"]
		// def awk_dedup_options = modules["awk_dedup"]

		// // Reporting options
		// def bedtools_intersect_options = modules["bedtools_intersect"]
		// bedtools_intersect_options.args = "-C -sorted"

		// // Multi QC
		// def multiqc_options = modules["multiqc"]
		// multiqc_options.args += params.multiqc_title ? " --title \"$params.multiqc_title\"" : ""

		/*
		========================================================================================
		IMPORT LOCAL MODULES/SUBWORKFLOWS
		@@ -104,13 +91,13 @@ include { AWK as AWK_FRAG_BIN } from "../modules/local/linux/awk"
		include { SAMTOOLS_CUSTOMVIEW } from "../modules/local/samtools_custom_view"
		include { IGV_SESSION } from "../modules/local/python/igv_session"
		include { AWK as AWK_EDIT_PEAK_BED } from "../modules/local/linux/awk"
		// include { CALCULATE_FRIP } from "../modules/local/modules/calculate_frip/main" addParams( options: modules["calc_frip"] )
		// include { CUT as CUT_CALC_REPROD } from "../modules/local/linux/cut" addParams( options: modules["calc_peak_repro_cut"] )
		// include { CALCULATE_PEAK_REPROD } from "../modules/local/modules/calculate_peak_reprod/main" addParams( options: modules["calc_peak_repro"] )
		// 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/modules/generate_reports/main" addParams( options: modules["generate_reports"] )
		// include { MULTIQC } from "../modules/local/multiqc" addParams( options: multiqc_options )
		include { CALCULATE_FRIP } from "../modules/local/modules/calculate_frip/main"
		include { CUT as CUT_CALC_REPROD } from "../modules/local/linux/cut"
		include { CALCULATE_PEAK_REPROD } from "../modules/local/modules/calculate_peak_reprod/main"
		include { EXPORT_META } from "../modules/local/export_meta"
		include { EXPORT_META as EXPORT_META_CTRL } from "../modules/local/export_meta"
		include { GENERATE_REPORTS } from "../modules/local/modules/generate_reports/main"
		include { MULTIQC } from "../modules/local/multiqc"

		/*
		* SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
		@@ -124,8 +111,8 @@ include { ANNOTATE_META_AWK as ANNOTATE_DEDUP_META } from "../subworkflows
		include { CONSENSUS_PEAKS } from "../subworkflows/local/consensus_peaks"
		include { CONSENSUS_PEAKS as CONSENSUS_PEAKS_ALL } from "../subworkflows/local/consensus_peaks"
		include { CALCULATE_FRAGMENTS } from "../subworkflows/local/calculate_fragments"
		// include { ANNOTATE_META_CSV as ANNOTATE_FRIP_META } from "../subworkflows/local/annotate_meta_csv" addParams( options: modules["meta_csv_frip_options"] )
		// include { ANNOTATE_META_CSV as ANNOTATE_PEAK_REPRO_META } from "../subworkflows/local/annotate_meta_csv" addParams( options: modules["meta_csv_peak_repro_options"] )
		include { ANNOTATE_META_CSV as ANNOTATE_FRIP_META } from "../subworkflows/local/annotate_meta_csv"
		include { ANNOTATE_META_CSV as ANNOTATE_PEAK_REPRO_META } from "../subworkflows/local/annotate_meta_csv"

		/*
		========================================================================================
		@@ -149,7 +136,7 @@ include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_GENE } from "../mo
		include { DEEPTOOLS_COMPUTEMATRIX as DEEPTOOLS_COMPUTEMATRIX_PEAKS } from "../modules/nf-core/modules/deeptools/computematrix/main"
		include { DEEPTOOLS_PLOTHEATMAP as DEEPTOOLS_PLOTHEATMAP_GENE } from "../modules/nf-core/modules/deeptools/plotheatmap/main"
		include { DEEPTOOLS_PLOTHEATMAP as DEEPTOOLS_PLOTHEATMAP_PEAKS } from "../modules/nf-core/modules/deeptools/plotheatmap/main"
		// include { BEDTOOLS_INTERSECT } from "../modules/nf-core/modules/bedtools/intersect/main.nf" addParams( options: bedtools_intersect_options )
		include { BEDTOOLS_INTERSECT } from "../modules/nf-core/modules/bedtools/intersect/main.nf"
		include { CUSTOM_DUMPSOFTWAREVERSIONS } from "../modules/local/modules/custom/dumpsoftwareversions/main"

		/*
		@@ -382,8 +369,8 @@ workflow CUTANDRUN {
		ch_samtools_bam,
		ch_markduplicates_metrics,
		ch_dummy_file.collect(),
		"",
		"dedup_",
		"",
		false
		)
		ch_samtools_bam = ANNOTATE_DEDUP_META.out.output
		@@ -866,139 +853,143 @@ workflow CUTANDRUN {
		/*
		* CHANNEL: Join bams and beds on id
		*/
		// ch_samtools_bam
		// .map { row -> [row[0].id, row ].flatten()}
		// .join ( ch_samtools_bai.map { row -> [row[0].id, row ].flatten()} )
		// .join ( ch_peaks_bed.map { row -> [row[0].id, row ].flatten()} )
		// .map { row -> [row[1], row[2], row[4], row[6]] }
		// .set { ch_bam_bai_bed }
		ch_samtools_bam
		.map { row -> [row[0].id, row ].flatten()}
		.join ( ch_samtools_bai.map { row -> [row[0].id, row ].flatten()} )
		.join ( ch_peaks_bed.map { row -> [row[0].id, row ].flatten()} )
		.map { row -> [row[1], row[2], row[4], row[6]] }
		.set { ch_bam_bai_bed }
		// EXAMPLE CHANNEL STRUCT: [[META], BAM, BAI, BED]
		//ch_bam_bai_bed \| view

		/*
		* MODULE: Calculate Frip scores for samples
		*/
		// CALCULATE_FRIP (
		// ch_bam_bai_bed
		// )
		// ch_software_versions = ch_software_versions.mix(CALCULATE_FRIP.out.versions)
		CALCULATE_FRIP (
		ch_bam_bai_bed
		)
		ch_software_versions = ch_software_versions.mix(CALCULATE_FRIP.out.versions)

		/*
		* SUBWORKFLOW: Annotate meta-data with frip stats
		*/
		// ANNOTATE_FRIP_META (
		// ch_samtools_bam,
		// CALCULATE_FRIP.out.frips
		// )
		// ch_samtools_bam_ctrl = ch_samtools_bam
		// ch_samtools_bam = ANNOTATE_FRIP_META.out.output
		ANNOTATE_FRIP_META (
		ch_samtools_bam,
		CALCULATE_FRIP.out.frips,
		"",
		""
		)
		ch_samtools_bam_ctrl = ch_samtools_bam
		ch_samtools_bam = ANNOTATE_FRIP_META.out.output
		//ch_samtools_bam \| view

		/*
		* MODULE: Trim unwanted columns for downstream reporting
		*/
		// CUT_CALC_REPROD (
		// AWK_NAME_PEAK_BED.out.file
		// )
		CUT_CALC_REPROD (
		AWK_NAME_PEAK_BED.out.file
		)

		/*
		* CHANNEL: Group samples based on group
		*/
		// CUT_CALC_REPROD.out.file
		// .map { row -> [ row[0].group, row[1] ] }
		// .groupTuple(by: [0])
		// .map { row ->
		// new_meta = [:]
		// new_meta.put( "id", row[0] )
		// [ new_meta, row[1].flatten() ]
		// }
		// .map { row ->
		// [ row[0], row[1], row[1].size() ]
		// }
		// .filter { row -> row[2] > 1 }
		// .map { row ->
		// [ row[0], row[1] ]
		// }
		// .set { ch_seacr_bed_group_2 }
		CUT_CALC_REPROD.out.file
		.map { row -> [ row[0].group, row[1] ] }
		.groupTuple(by: [0])
		.map { row ->
		new_meta = [:]
		new_meta.put( "id", row[0] )
		[ new_meta, row[1].flatten() ]
		}
		.map { row ->
		[ row[0], row[1], row[1].size() ]
		}
		.filter { row -> row[2] > 1 }
		.map { row ->
		[ row[0], row[1] ]
		}
		.set { ch_seacr_bed_group_2 }

		/*
		* CHANNEL: Per group, create a channel per one against all combination
		*/
		// ch_seacr_bed_group_2
		// .flatMap{
		// row ->
		// new_output = []
		// row[1].each{ file ->
		// files_copy = row[1].collect()
		// files_copy.remove(files_copy.indexOf(file))
		// new_output.add([[id: file.name.split("\\.")[0]], file, files_copy])
		// }
		// new_output
		// }
		// .set { ch_beds_intersect }
		ch_seacr_bed_group_2
		.flatMap{
		row ->
		new_output = []
		row[1].each{ file ->
		files_copy = row[1].collect()
		files_copy.remove(files_copy.indexOf(file))
		new_output.add([[id: file.name.split("\\.")[0]], file, files_copy])
		}
		new_output
		}
		.set { ch_beds_intersect }
		//EXAMPLE CHANNEL STRUCT: [[META], BED (-a), [BED...n] (-b)]
		//ch_beds_intersect \| view

		/*
		* MODULE: Find intra-group overlap
		*/
		// BEDTOOLS_INTERSECT (
		// ch_beds_intersect,
		// "bed"
		// )
		// ch_software_versions = ch_software_versions.mix(BEDTOOLS_INTERSECT.out.versions)
		BEDTOOLS_INTERSECT (
		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

		/*
		* MODULE: Use overlap to calculate a peak repro %
		*/
		// CALCULATE_PEAK_REPROD (
		// BEDTOOLS_INTERSECT.out.intersect
		// )
		// ch_software_versions = ch_software_versions.mix(CALCULATE_PEAK_REPROD.out.versions)
		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

		/*
		* SUBWORKFLOW: Annotate meta-data with peak stats
		*/
		// ANNOTATE_PEAK_REPRO_META (
		// ch_samtools_bam,
		// CALCULATE_PEAK_REPROD.out.csv
		// )
		// ch_samtools_bam = ANNOTATE_PEAK_REPRO_META.out.output
		ANNOTATE_PEAK_REPRO_META (
		ch_samtools_bam,
		CALCULATE_PEAK_REPROD.out.csv,
		"",
		""
		)
		ch_samtools_bam = ANNOTATE_PEAK_REPRO_META.out.output
		//ch_samtools_bam \| view

		/*
		* MODULE: Export meta-data to csv file
		*/
		// EXPORT_META (
		// ch_samtools_bam.collect{it[0]},
		// "meta_table"
		// )
		EXPORT_META (
		ch_samtools_bam.collect{it[0]},
		"meta_table"
		)

		/*
		* MODULE: Export meta-data to csv file
		*/
		// EXPORT_META_CTRL (
		// ch_samtools_bam_ctrl.collect{it[0]},
		// "meta_table_ctrl"
		// )
		EXPORT_META_CTRL (
		ch_samtools_bam_ctrl.collect{it[0]},
		"meta_table_ctrl"
		)

		/*
		* MODULE: Generate python reporting using mixture of meta-data and direct file processing
		*/
		// GENERATE_REPORTS(
		// EXPORT_META.out.csv.collect().ifEmpty([]), // meta-data report stats
		// EXPORT_META_CTRL.out.csv, // meta-data report stats
		// SAMTOOLS_CUSTOMVIEW.out.tsv.collect{it[1]}, // raw fragments
		// AWK_FRAG_BIN.out.file.collect{it[1]}, // binned fragments
		// ch_peaks_bed.collect{it[1]}, // peak beds
		// ch_frag_len_header_multiqc // multiqc config header for fragment length distribution plot
		// )
		// ch_frag_len_multiqc = GENERATE_REPORTS.out.frag_len_multiqc
		// ch_software_versions = ch_software_versions.mix(GENERATE_REPORTS.out.versions)
		GENERATE_REPORTS(
		EXPORT_META.out.csv.collect().ifEmpty([]), // meta-data report stats
		EXPORT_META_CTRL.out.csv, // meta-data report stats
		SAMTOOLS_CUSTOMVIEW.out.tsv.collect{it[1]}, // raw fragments
		AWK_FRAG_BIN.out.file.collect{it[1]}, // binned fragments
		ch_peaks_bed.collect{it[1]}, // peak beds
		ch_frag_len_header_multiqc // multiqc config header for fragment length distribution plot
		)
		ch_frag_len_multiqc = GENERATE_REPORTS.out.frag_len_multiqc
		ch_software_versions = ch_software_versions.mix(GENERATE_REPORTS.out.versions)
		}

		/*

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