Modules config now uses "${params.publish_dir_mode}" instead of copy (30707ace) · Commits · Chaos / Cutandrun

conf/modules.config

+55 −55

Original line number	Diff line number	Diff line
		@@ -19,14 +19,14 @@
		process {
		publishDir = [
		path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
		]

		withName: CUSTOM_DUMPSOFTWAREVERSIONS {
		publishDir = [
		path: { "${params.outdir}/pipeline_info" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: '*_versions.yml'
		]
		}
		@@ -43,7 +43,7 @@ if(params.run_input_check) {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:INPUT_CHECK:SAMPLESHEET_CHECK' {
		publishDir = [
		path: { "${params.outdir}/pipeline_info" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
		]
		}
		@@ -61,7 +61,7 @@ if (params.run_genome_prep) {
		withName: '.PREPARE_GENOME:GUNZIP_.' {
		publishDir = [
		path: { "${params.outdir}/00_genome" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: params.save_reference
		]
		@@ -74,7 +74,7 @@ if (params.run_genome_prep) {
		withName: '.*CHROMSIZES' {
		publishDir = [
		path: { "${params.outdir}/00_genome" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: params.save_reference
		]
		@@ -83,7 +83,7 @@ if (params.run_genome_prep) {
		withName: 'UNTAR_INDEX_.*\|TARGET\|SPIKEIN' {
		publishDir = [
		path: { "${params.outdir}/00_genome/index" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: params.save_reference
		]
		@@ -92,7 +92,7 @@ if (params.run_genome_prep) {
		withName: 'BOWTIE2_BUILD_.*\|TARGET\|SPIKEIN' {
		publishDir = [
		path: { "${params.outdir}/00_genome/index" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: params.save_reference
		]
		@@ -111,7 +111,7 @@ if(params.run_cat_fastq) {
		withName: 'CAT_FASTQ' {
		publishDir = [
		path: { "${params.outdir}/01_prealign/merged_fastq" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: params.save_merged_fastq
		]
		@@ -125,7 +125,7 @@ if(params.run_trim_galore_fastqc && !params.skip_fastqc) {
		ext.args = '--quiet'
		publishDir = [
		path: { "${params.outdir}/01_prealign/pretrim_fastqc" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		]
		}
		@@ -142,18 +142,18 @@ if(params.run_trim_galore_fastqc && !params.skip_trimming) {
		publishDir = [
		[
		path: { "${params.outdir}/01_prealign/trimgalore/fastqc" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.{html,zip}"
		],
		[
		path: { "${params.outdir}/01_prealign/trimgalore" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.fastq.gz",
		enabled: params.save_trimmed
		],
		[
		path: { "${params.outdir}/01_prealign/trimgalore" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.txt"
		]
		]
		@@ -174,18 +174,18 @@ if(params.run_alignment) {
		publishDir = [
		[
		path: { "${params.outdir}/02_alignment/${params.aligner}/target/log" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: '*.log'
		],
		[
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: '*.bam',
		enabled: ( params.save_align_intermed \|\| (!params.run_q_filter && !params.run_mark_dups && !params.run_remove_dups) )
		],
		[
		path: { "${params.outdir}/02_alignment/${params.aligner}/target/unmapped" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: '*.fastq.gz',
		enabled: params.save_unaligned
		]
		@@ -198,18 +198,18 @@ if(params.run_alignment) {
		publishDir = [
		[
		path: { "${params.outdir}/02_alignment/${params.aligner}/spikein/log" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: '*.log'
		],
		[
		path: { "${params.outdir}/02_alignment/${params.aligner}/spikein" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: '*.bam',
		enabled: params.save_spikein_aligned
		],
		[
		path: { "${params.outdir}/02_alignment/${params.aligner}/spikein/unmapped" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: '*.fastq.gz',
		enabled: ( params.save_spikein_aligned && params.save_unaligned )
		]
		@@ -219,7 +219,7 @@ if(params.run_alignment) {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.:BAM_SORT_SAMTOOLS:BAM_STATS_SAMTOOLS:.' {
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.{stats,flagstat,idxstats}",
		enabled: ( params.save_align_intermed \|\| (!params.run_q_filter && !params.run_mark_dups && !params.run_remove_dups) )
		]
		@@ -228,7 +228,7 @@ if(params.run_alignment) {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.:BAM_SORT_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:.' {
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/spikein" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.{stats,flagstat,idxstats}",
		enabled: params.save_spikein_aligned
		]
		@@ -238,7 +238,7 @@ if(params.run_alignment) {
		ext.prefix = { "${meta.id}.target.sorted" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bam",
		enabled: ( params.save_align_intermed \|\| (!params.run_q_filter && !params.run_mark_dups && !params.run_remove_dups) )
		]
		@@ -248,7 +248,7 @@ if(params.run_alignment) {
		ext.prefix = { "${meta.id}.spikein.sorted" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/spikein" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bam",
		enabled: params.save_spikein_aligned
		]
		@@ -258,7 +258,7 @@ if(params.run_alignment) {
		ext.prefix = { "${meta.id}.target.sorted" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bai",
		enabled: ( params.save_align_intermed \|\| (!params.run_q_filter && !params.run_mark_dups && !params.run_remove_dups) )
		]
		@@ -268,7 +268,7 @@ if(params.run_alignment) {
		ext.prefix = { "${meta.id}.spikein.sorted" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/spikein" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bai",
		enabled: params.save_spikein_aligned
		]
		@@ -289,7 +289,7 @@ if(params.run_q_filter) {
		ext.prefix = { "${meta.id}.target.filtered" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bam",
		enabled: ( params.save_align_intermed \|\| (!params.run_mark_dups && !params.run_remove_dups) )
		]
		@@ -299,7 +299,7 @@ if(params.run_q_filter) {
		ext.prefix = { "${meta.id}.target.filtered.sorted" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bam",
		enabled: ( params.save_align_intermed \|\| (!params.run_mark_dups && !params.run_remove_dups) )
		]
		@@ -309,7 +309,7 @@ if(params.run_q_filter) {
		ext.prefix = { "${meta.id}.target.filtered" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bai",
		enabled: ( params.save_align_intermed \|\| (!params.run_mark_dups && !params.run_remove_dups) )
		]
		@@ -319,7 +319,7 @@ if(params.run_q_filter) {
		ext.prefix = { "${meta.id}.target.filtered" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.{stats,flagstat,idxstats}",
		enabled: ( params.save_align_intermed \|\| (!params.run_mark_dups && !params.run_remove_dups) )
		]
		@@ -340,7 +340,7 @@ if(params.run_mark_dups) {
		ext.prefix = { "${meta.id}.target.markdup" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bam",
		enabled: ( params.save_align_intermed \|\| (!params.run_remove_dups) \|\| (!params.dedup_target_reads) )
		]
		@@ -349,7 +349,7 @@ if(params.run_mark_dups) {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:MARK_DUPLICATES_PICARD:SAMTOOLS_INDEX' {
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bai",
		enabled: ( params.save_align_intermed \|\| (!params.run_remove_dups) )
		]
		@@ -358,7 +358,7 @@ if(params.run_mark_dups) {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:MARK_DUPLICATES_PICARD:BAM_STATS_SAMTOOLS:.*' {
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.{stats,flagstat,idxstats}",
		enabled: ( params.save_align_intermed \|\| (!params.run_remove_dups) )
		]
		@@ -373,7 +373,7 @@ if(params.run_remove_dups) {
		ext.prefix = { "${meta.id}.target.dedup" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bam",
		enabled: true
		]
		@@ -382,7 +382,7 @@ if(params.run_remove_dups) {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEDUPLICATE_PICARD:SAMTOOLS_INDEX' {
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bai",
		enabled: true
		]
		@@ -391,7 +391,7 @@ if(params.run_remove_dups) {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEDUPLICATE_PICARD:BAM_STATS_SAMTOOLS:.*' {
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.{stats,flagstat,idxstats}",
		enabled: true
		]
		@@ -476,7 +476,7 @@ if(params.run_peak_calling) {
		ext.prefix = { "${meta.id}.sorted" }
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/01_bam_to_bedgraph" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bedGraph",
		enabled: true
		]
		@@ -486,7 +486,7 @@ if(params.run_peak_calling) {
		ext.prefix = { "${meta.id}.clipped" }
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/02_clip_bed" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bedGraph",
		enabled: true
		]
		@@ -495,7 +495,7 @@ if(params.run_peak_calling) {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:UCSC_BEDGRAPHTOBIGWIG' {
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/03_bed_to_bigwig" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bigWig",
		enabled: true
		]
		@@ -510,7 +510,7 @@ if(params.run_peak_calling && 'seacr' in params.callers) {
		ext.prefix = { "${meta.id}.seacr.peaks.bed" }
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/04_called_peaks" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bed",
		enabled: true
		]
		@@ -525,7 +525,7 @@ if(params.run_peak_calling && 'macs2' in params.callers) {
		ext.prefix = { "${meta.id}.macs2.peaks.bed" }
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/04_called_peaks" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		pattern: "*.bed",
		enabled: true
		]
		@@ -562,7 +562,7 @@ if(params.run_peak_calling) {
		ext.prefix = { "${meta.id}.consensus.peaks" }
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/05_consensus_peaks" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		@@ -571,7 +571,7 @@ if(params.run_peak_calling) {
		withName: '.:CONSENSUS_PEAKS:PLOT_CONSENSUS_PEAKS\|.:CONSENSUS_PEAKS_ALL:PLOT_CONSENSUS_PEAKS' {
		publishDir = [
		path: { "${params.outdir}/04_reporting" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: params.skip_upset_plots
		]
		@@ -587,7 +587,7 @@ if(params.run_peak_calling && !params.run_consensus_all) {
		ext.suffix = ".consensus.peaks.filtered"
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/05_consensus_peaks" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		@@ -602,7 +602,7 @@ if(params.run_peak_calling && params.run_consensus_all) {
		ext.ext = "bed"
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/05_consensus_peaks" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		@@ -657,7 +657,7 @@ if(params.run_peak_calling) {
		ext.ext = "bed"
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/06_fragments" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		@@ -671,7 +671,7 @@ if(params.run_peak_calling) {
		ext.ext = "bed"
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/06_fragments" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		@@ -683,7 +683,7 @@ if(params.run_peak_calling) {
		ext.suffix = ".frags.len"
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/06_fragments" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		@@ -702,7 +702,7 @@ if(params.run_reporting && params.run_igv) {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:IGV_SESSION' {
		publishDir = [
		path: { "${params.outdir}/04_reporting/igv" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		@@ -724,7 +724,7 @@ if(params.run_reporting && params.run_deep_tools) {
		ext.args = "scale-regions --beforeRegionStartLength 3000 --regionBodyLength 5000 --afterRegionStartLength 3000 --skipZeros --missingDataAsZero"
		publishDir = [
		path: { "${params.outdir}/04_reporting/heatmaps/gene" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		@@ -734,7 +734,7 @@ if(params.run_reporting && params.run_deep_tools) {
		ext.args = "--sortUsing sum"
		publishDir = [
		path: { "${params.outdir}/04_reporting/heatmaps/gene" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		@@ -744,7 +744,7 @@ if(params.run_reporting && params.run_deep_tools) {
		ext.args = "reference-point -a 3000 -b 3000 --referencePoint center --skipZeros --missingDataAsZero"
		publishDir = [
		path: { "${params.outdir}/04_reporting/heatmaps/peaks" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		@@ -754,7 +754,7 @@ if(params.run_reporting && params.run_deep_tools) {
		ext.args = "--sortUsing sum --startLabel \"Peak Start\" --endLabel \"Peak End\" --xAxisLabel \"\" --regionsLabel \"Peaks\""
		publishDir = [
		path: { "${params.outdir}/04_reporting/heatmaps/peaks" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		@@ -795,7 +795,7 @@ if(params.run_reporting) {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:EXPORT_META' {
		publishDir = [
		path: { "${params.outdir}/04_reporting" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		@@ -804,7 +804,7 @@ if(params.run_reporting) {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:EXPORT_META_CTRL' {
		publishDir = [
		path: { "${params.outdir}/04_reporting" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		@@ -813,7 +813,7 @@ if(params.run_reporting) {
		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:GENERATE_REPORTS' {
		publishDir = [
		path: { "${params.outdir}/04_reporting/qc" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		@@ -830,7 +830,7 @@ if (params.run_multiqc) {
		ext.args = params.multiqc_title ? "-v --title \"$params.multiqc_title\"" : '-v'
		publishDir = [
		path: { "${params.outdir}/04_reporting/multiqc" },
		mode: 'copy',
		mode: "${params.publish_dir_mode}",
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
		]
		}

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