Fixed tests (2c927054) · Commits · Chaos / Cutandrun

conf/modules.config

+8 −5

Original line number	Diff line number	Diff line
		@@ -194,6 +194,7 @@ if(params.run_alignment) {

		withName: '.*:ALIGN_BOWTIE2:BOWTIE2_SPIKEIN_ALIGN' {
		ext.args = '--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant --phred33 -I 10 -X 700'
		ext.prefix = { "${meta.id}.spikein" }
		publishDir = [
		[
		path: { "${params.outdir}/02_alignment/${params.aligner}/spikein/log" },
		@@ -204,7 +205,7 @@ if(params.run_alignment) {
		path: { "${params.outdir}/02_alignment/${params.aligner}/spikein" },
		mode: 'copy',
		pattern: '*.bam',
		enabled: ( params.save_spikein_aligned && ( params.save_align_intermed \|\| (!params.run_q_filter && !params.run_mark_dups && !params.run_remove_dups) ) )
		enabled: params.save_spikein_aligned
		],
		[
		path: { "${params.outdir}/02_alignment/${params.aligner}/spikein/unmapped" },
		@@ -229,7 +230,7 @@ if(params.run_alignment) {
		path: { "${params.outdir}/02_alignment/${params.aligner}/spikein" },
		mode: 'copy',
		pattern: "*.{stats,flagstat,idxstats}",
		enabled: ( params.save_spikein_aligned && ( params.save_align_intermed \|\| (!params.run_q_filter && !params.run_mark_dups && !params.run_remove_dups) ) )
		enabled: params.save_spikein_aligned
		]
		}

		@@ -249,11 +250,12 @@ if(params.run_alignment) {
		path: { "${params.outdir}/02_alignment/${params.aligner}/spikein" },
		mode: 'copy',
		pattern: "*.bam",
		enabled: ( params.save_spikein_aligned && ( params.save_align_intermed \|\| (!params.run_q_filter && !params.run_mark_dups && !params.run_remove_dups) ) )
		enabled: params.save_spikein_aligned
		]
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:BAM_SORT_SAMTOOLS:SAMTOOLS_INDEX' {
		ext.prefix = { "${meta.id}.target.sorted" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/target" },
		mode: 'copy',
		@@ -263,11 +265,12 @@ if(params.run_alignment) {
		}

		withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:BAM_SORT_SAMTOOLS_SPIKEIN:SAMTOOLS_INDEX' {
		ext.prefix = { "${meta.id}.spikein.sorted" }
		publishDir = [
		path: { "${params.outdir}/02_alignment/${params.aligner}/spikein" },
		mode: 'copy',
		pattern: "*.bam",
		enabled: ( params.save_spikein_aligned && ( params.save_align_intermed \|\| (!params.run_q_filter && !params.run_mark_dups && !params.run_remove_dups) ) )
		pattern: "*.bai",
		enabled: params.save_spikein_aligned
		]
		}
		}

tests/test_verify_output_save_spikein_align.yml

+2 −2

Original line number	Diff line number	Diff line
		@@ -9,5 +9,5 @@
		- path: results/02_alignment/bowtie2/spikein/igg_R1.spikein.sorted.bam
		- path: results/02_alignment/bowtie2/spikein/h3k27me3_R1.spikein.sorted.bam.bai
		- path: results/02_alignment/bowtie2/spikein/igg_R1.spikein.sorted.bam.bai
		- path: results/02_alignment/bowtie2/spikein/samtools_stats/h3k27me3_R1.spikein.sorted.bam.flagstat
		- path: results/02_alignment/bowtie2/spikein/samtools_stats/igg_R1.spikein.sorted.bam.flagstat
		No newline at end of file
		- path: results/02_alignment/bowtie2/spikein/h3k27me3_R1.spikein.sorted.bam.flagstat
		- path: results/02_alignment/bowtie2/spikein/igg_R1.spikein.sorted.bam.flagstat
		No newline at end of file

tests/test_verify_output_save_unaligned.yml

+4 −4

Original line number	Diff line number	Diff line
		@@ -5,7 +5,7 @@
		- verify_output_align
		- verify_output_align_save_unaligned
		files:
		- path: results/02_alignment/bowtie2/target/unmapped/h3k27me3_R1.target.unmapped_1.fastq.gz
		- path: results/02_alignment/bowtie2/target/unmapped/igg_R1.target.unmapped_2.fastq.gz
		- path: results/02_alignment/bowtie2/target/unmapped/h3k27me3_R1.target.unmapped_1.fastq.gz
		- path: results/02_alignment/bowtie2/target/unmapped/igg_R1.target.unmapped_2.fastq.gz
		No newline at end of file
		- path: results/02_alignment/bowtie2/target/unmapped/h3k27me3_R1.unmapped_1.fastq.gz
		- path: results/02_alignment/bowtie2/target/unmapped/igg_R1.unmapped_2.fastq.gz
		- path: results/02_alignment/bowtie2/target/unmapped/h3k27me3_R1.unmapped_1.fastq.gz
		- path: results/02_alignment/bowtie2/target/unmapped/igg_R1.unmapped_2.fastq.gz
		No newline at end of file

tests/test_verify_output_skip_reporting.yml

+2 −2

Original line number	Diff line number	Diff line
		@@ -28,7 +28,7 @@
		should_exist: false

		- name: test_verify_output_skip_reporting_heatmaps
		command: nextflow run main.nf -profile docker,test --skip_fastqc true --skip_reporting true
		command: nextflow run main.nf -profile docker,test --skip_fastqc true --skip_heatmaps true
		tags:
		- verify_output
		- verify_output_reporting
		@@ -41,7 +41,7 @@
		- path: results/06_reporting/heatmaps/igv/igv_session.xml

		- name: test_verify_output_skip_reporting_multiqc
		command: nextflow run main.nf -profile docker,test --skip_fastqc true --skip_reporting true
		command: nextflow run main.nf -profile docker,test --skip_fastqc true --skip_multiqc true
		tags:
		- verify_output
		- verify_output_reporting

workflows/cutandrun.nf

+8 −8

Original line number	Diff line number	Diff line
		@@ -748,8 +748,6 @@ workflow CUTANDRUN {
		//SAMTOOLS_CUSTOMVIEW.out.tsv \| view
		}

		if(params.run_reporting) {
		if(params.run_igv) {
		/*
		* CHANNEL: Remove IgG from bigwig channel
		*/
		@@ -758,6 +756,8 @@ workflow CUTANDRUN {
		.set { ch_bigwig_no_igg }
		//ch_bigwig_no_igg \| view

		if(params.run_reporting) {
		if(params.run_igv) {
		/*
		* MODULE: Create igv session
		*/

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