Reporting working (2af69f8a) · Commits · Chaos / Cutandrun

assets/multiqc_config.yaml

+2 −2

Original line number	Diff line number	Diff line
		@@ -37,11 +37,11 @@ module_order:
		- bowtie2:
		name: 'Bowtie2 (target)'
		path_filters:
		- "./bowtie2/*target.bowtie2.log"
		- "./bowtie2/*.bowtie2.log"
		- bowtie2:
		name: 'Bowtie2 (spike-in)'
		path_filters:
		- "./bowtie2/*spikein.bowtie2.log"
		- "./bowtie2_spikein/*.bowtie2.log"
		- samtools
		- picard
		- custom_content

conf/modules.config

+14 −26

Original line number	Diff line number	Diff line
		@@ -630,6 +630,7 @@ if(params.run_peak_calling) {
		ext.command = "'{print \$1, int((\$2 + \$3)/(2w))w + w/2, FILENAME}'"
		ext.command2 = "\| sort -T '.' -k1,1V -k2,2n \| uniq -c \| awk -v OFS=\"\\t\" '{print \$2, \$3, \$1, \$4}' \| sort -T '.' -k1,1V -k2,2n"
		ext.suffix = ".frags.bin500"
		ext.ext = "bed"
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/06_fragments" },
		mode: 'copy',
		@@ -785,28 +786,15 @@ if(params.run_reporting) {
		}
		}


		// 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 \"$params.multiqc_title\"" : ""
		No newline at end of file
		if (!params.run_multiqc) {
		process {
		withName: "NFCORE_CUTANDRUN:CUTANDRUN:MULTIQC" {
		ext.args = params.multiqc_title ? "-v --title \"$params.multiqc_title\"" : '-v'
		publishDir = [
		path: { "${params.outdir}/04_reporting/multiqc" },
		mode: 'copy',
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
		]
		}
		}
		}

modules/local/modules/generate_reports/main.nf

+1 −1

Original line number	Diff line number	Diff line
		@@ -29,7 +29,7 @@ process GENERATE_REPORTS {
		reporting.py gen_reports \\
		--meta $meta_data_resolved \\
		--meta_ctrl $meta_data_ctrl \\
		--raw_frag "*.frag_len.txt" \\
		--raw_frag "*.frags.len.txt" \\
		--bin_frag "*bin500.awk.bed" \\
		--seacr_bed "bed.bed" \\
		--output . \\

modules/local/multiqc.nf

+1 −1

Original line number	Diff line number	Diff line
		@@ -16,7 +16,7 @@ process MULTIQC {
		path ('trimgalore/fastqc/*')
		path ('trimgalore/*')
		path ('bowtie2/*')
		path ('bowtie2/*')
		path ('bowtie2_spikein/*')
		path ('samtools/stats/*')
		path ('samtools/flagstat/*')
		path ('samtools/idxstats/*')

workflows/cutandrun.nf

+23 −23

Original line number	Diff line number	Diff line
		@@ -1002,29 +1002,29 @@ workflow CUTANDRUN {
		/*
		* MODULE: Multiqc
		*/
		// if (run_multiqc) {
		// workflow_summary = WorkflowCutandrun.paramsSummaryMultiqc(workflow, summary_params)
		// ch_workflow_summary = Channel.value(workflow_summary)

		// MULTIQC (
		// ch_multiqc_config,
		// ch_multiqc_custom_config.collect().ifEmpty([]),
		// CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect(),
		// CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_unique_yml.collect(),
		// ch_workflow_summary.collectFile(name: "workflow_summary_mqc.yaml"),
		// FASTQC_TRIMGALORE.out.fastqc_zip.collect{it[1]}.ifEmpty([]),
		// FASTQC_TRIMGALORE.out.trim_zip.collect{it[1]}.ifEmpty([]),
		// FASTQC_TRIMGALORE.out.trim_log.collect{it[1]}.ifEmpty([]),
		// ch_bowtie2_log.collect{it[1]}.ifEmpty([]),
		// ch_bowtie2_spikein_log.collect{it[1]}.ifEmpty([]),
		// ch_samtools_stats.collect{it[1]}.ifEmpty([]),
		// ch_samtools_flagstat.collect{it[1]}.ifEmpty([]),
		// ch_samtools_idxstats.collect{it[1]}.ifEmpty([]),
		// ch_markduplicates_metrics.collect{it[1]}.ifEmpty([]),
		// ch_frag_len_multiqc.collect().ifEmpty([])
		// )
		// multiqc_report = MULTIQC.out.report.toList()
		// }
		if (params.run_multiqc) {
		workflow_summary = WorkflowCutandrun.paramsSummaryMultiqc(workflow, summary_params)
		ch_workflow_summary = Channel.value(workflow_summary)

		MULTIQC (
		ch_multiqc_config,
		ch_multiqc_custom_config.collect().ifEmpty([]),
		CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect(),
		CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_unique_yml.collect(),
		ch_workflow_summary.collectFile(name: "workflow_summary_mqc.yaml"),
		FASTQC_TRIMGALORE.out.fastqc_zip.collect{it[1]}.ifEmpty([]),
		FASTQC_TRIMGALORE.out.trim_zip.collect{it[1]}.ifEmpty([]),
		FASTQC_TRIMGALORE.out.trim_log.collect{it[1]}.ifEmpty([]),
		ch_bowtie2_log.collect{it[1]}.ifEmpty([]),
		ch_bowtie2_spikein_log.collect{it[1]}.ifEmpty([]),
		ch_samtools_stats.collect{it[1]}.ifEmpty([]),
		ch_samtools_flagstat.collect{it[1]}.ifEmpty([]),
		ch_samtools_idxstats.collect{it[1]}.ifEmpty([]),
		ch_markduplicates_metrics.collect{it[1]}.ifEmpty([]),
		ch_frag_len_multiqc.collect().ifEmpty([])
		)
		multiqc_report = MULTIQC.out.report.toList()
		}
		}

		////////////////////////////////////////////////////

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