fix peak calling tests (197dae1d) · Commits · Chaos / Cutandrun

conf/modules.config

+9 −3

Original line number	Diff line number	Diff line
		@@ -119,7 +119,7 @@ if(params.run_cat_fastq) {
		}
		}

		if(params.run_trim_galore_fastqc) {
		if(params.run_trim_galore_fastqc && !params.skip_fastqc) {
		process {
		withName: '.*:FASTQC_TRIMGALORE:FASTQC' {
		ext.args = '--quiet'
		@@ -129,7 +129,11 @@ if(params.run_trim_galore_fastqc) {
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		]
		}
		}
		}

		if(params.run_trim_galore_fastqc && !params.skip_trimming) {
		process {
		withName: '.*:FASTQC_TRIMGALORE:TRIMGALORE' {
		ext.args = [
		'--fastqc',
		@@ -459,7 +463,7 @@ if(params.run_peak_calling) {
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/03_bed_to_bigwig" },
		mode: 'copy',
		pattern: "*.bigwig",
		pattern: "*.bigWig",
		enabled: true
		]
		}
		@@ -522,13 +526,14 @@ if(params.run_peak_calling) {

		withName: '.:CONSENSUS_PEAKS:BEDTOOLS_MERGE\|.:CONSENSUS_PEAKS_ALL:BEDTOOLS_MERGE' {
		ext.args = " -c 2,3,4,5,6,7,7 -o collapse,collapse,collapse,collapse,collapse,collapse,count_distinct"
		ext.suffix = ".consensus.peaks"
		ext.prefix = { "${meta.id}.consensus.peaks" }
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/05_consensus_peaks" },
		mode: 'copy',
		saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
		enabled: true
		]
		cache = false
		}

		withName: '.:CONSENSUS_PEAKS:PLOT_CONSENSUS_PEAKS\|.:CONSENSUS_PEAKS_ALL:PLOT_CONSENSUS_PEAKS' {
		@@ -547,6 +552,7 @@ if(params.run_peak_calling && !params.run_consensus_all) {
		withName: '.*:CONSENSUS_PEAKS:AWK' {
		ext.command = "' \$10 >= 1 {print \$0}'"
		ext.ext = "bed"
		ext.suffix = ".consensus.peaks.filtered"
		publishDir = [
		path: { "${params.outdir}/03_peak_calling/05_consensus_peaks" },
		mode: 'copy',

tests/test_verify_output_only_peak_calling.yml

+1 −1

Original line number	Diff line number	Diff line
		@@ -16,6 +16,6 @@
		should_exist: false
		- path: results/03_peak_calling/05_consensus_peaks/h3k27me3.consensus.peaks.bed
		- path: results/03_peak_calling/05_consensus_peaks/h3k27me3.consensus.peaks.filtered.awk.bed
		- path: results/03_peak_calling/06_fragments/h3k27me3_R1.frag_len.txt
		- path: results/03_peak_calling/06_fragments/h3k27me3_R1.frags.len.txt
		- path: results/03_peak_calling/06_fragments/h3k27me3_R1.frags.bin500.awk.bed
		- path: results/03_peak_calling/06_fragments/h3k27me3_R1.frags.cut.bed
		No newline at end of file

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