Added peak caller tests (087b47f0) · Commits · Chaos / Cutandrun

tests/test_peak_callers.yml

0 → 100644

+49 −0

Original line number	Diff line number	Diff line
		- name: test_peak_callers_seacr
		command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller seacr -c tests/config/nextflow.config
		tags:
		- test_peak_callers
		- test_peak_callers_seacr
		files:
		- path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.seacr.peaks.bed.stringent.bed

		- name: test_peak_callers_macs2
		command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller macs2 -c tests/config/nextflow.config
		tags:
		- test_peak_callers
		- test_peak_callers_macs2
		files:
		- path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.macs2.peaks.bed_summits.bed

		- name: test_peak_callers_invalid_name
		command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller test -c tests/config/nextflow.config
		tags:
		- test_peak_callers
		- test_peak_callers_invalid
		exit_code: 1

		- name: test_peak_callers_seacr_macs2
		command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller seacr,macs2 -c tests/config/nextflow.config
		tags:
		- test_peak_callers
		- test_peak_callers_seacr_macs2
		files:
		- path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.seacr.peaks.bed.stringent.bed
		- path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.macs2.peaks.bed_summits.bed

		- name: test_peak_callers_macs2_seacr
		command: nextflow run main.nf -profile docker,test --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller macs2,seacr -c tests/config/nextflow.config
		tags:
		- test_peak_callers
		- test_peak_callers_macs2_seacr
		files:
		- path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.seacr.peaks.bed.stringent.bed
		- path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.macs2.peaks.bed_summits.bed

		- name: test_peak_callers_seacr_macs2_noigg
		command: nextflow run main.nf -profile docker,test_no_igg --only_peak_calling true --skip_fastqc true --skip_removeduplicates true --peakcaller seacr,macs2 -c tests/config/nextflow.config
		tags:
		- test_peak_callers
		- test_peak_callers_seacr_macs2_noigg
		files:
		- path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.seacr.peaks.bed.stringent.bed
		- path: results/03_peak_calling/04_called_peaks/h3k27me3_R1.macs2.peaks.bed_summits.bed

workflows/cutandrun.nf

+9 −1

Original line number	Diff line number	Diff line
		@@ -809,6 +809,14 @@ workflow CUTANDRUN {
		}

		if('macs2' in callers) {
		ch_samtools_bam
		.branch{ it ->
		target: it[0].group != "igg"
		control: it[0].group == "igg"
		}
		.set { ch_samtools_bam_split }
		// ch_samtools_bam_split.target \| view

		/*
		* CHANNEL: Add fake control channel
		*/
		@@ -816,7 +824,7 @@ workflow CUTANDRUN {
		.map{ row-> [ row[0], row[1], [] ] }
		.set { ch_samtools_bam_target_fctrl }
		// EXAMPLE CHANNEL STRUCT: [[META], BAM, FAKE_CTRL]
		ch_samtools_bam_target_fctrl \| view
		//ch_samtools_bam_target_fctrl \| view

		MACS2_CALLPEAK_NOIGG (
		ch_samtools_bam_target_fctrl,

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